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Started by upstream project "BIOFORMATS-test-repo" build number 296 originally caused by: Started by upstream project "Trigger" build number 315 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins2826250061494599879.sh + '[' flex = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_46795_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] 01:07:57,855 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:07:57,858 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 01:07:57,858 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:07:57,859 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:07:57,859 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:07:57,859 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:07:57,860 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:07:57,860 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:07:57,860 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:07:57,861 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:07:57,861 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:07:57,861 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:07:58,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:07:58,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:07:58,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:07:58,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:07:58,125 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:07:58,125 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:07:58,125 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:07:58,125 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:07:58,125 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 01:07:58,126 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 01:07:58,126 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 266 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-20 01:07:58,136] [main] java.version = 1.8.0_342 [testng] 01:07:58,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:07:58,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:07:58,183 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-20_01-07-58.log] [testng] 01:07:58,184 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-20 01:07:58,186] [main] testng.directory = /data [testng] [2024-12-20 01:07:58,187] [main] testng.configDirectory = /config [testng] [2024-12-20 01:07:58,199] [main] testng.multiplier = 1.0 [testng] [2024-12-20 01:07:58,199] [main] testng.in-memory = false [testng] [2024-12-20 01:07:58,199] [main] testng.allow-missing = false [testng] [2024-12-20 01:07:58,199] [main] user.language = en [testng] [2024-12-20 01:07:58,199] [main] user.country = ${user.country} [testng] [2024-12-20 01:07:58,199] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-20 01:10:13,375] [main] ---------------------------------------- [testng] [2024-12-20 01:10:13,375] [main] Total files: 791 [testng] [2024-12-20 01:10:13,376] [main] Scan time: 135.176 s (170 ms/file) [testng] [2024-12-20 01:10:13,376] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-20 01:17:26,171] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] 01:17:26,172 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:17:26,172 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:17:26,173 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-20_01-17-26.log] [testng] 01:17:26,173 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a0d8ea6 - End of configuration. [testng] [2024-12-20 01:17:27,961] [pool-1-thread-12] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] 01:17:27,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:17:27,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:17:27,962 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-20_01-17-27.log] [testng] 01:17:27,963 |-INFO in ch.qos.logback.core.sift.SiftProcessor@486b8630 - End of configuration. [testng] [2024-12-20 01:17:30,074] [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] 01:17:30,074 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:17:30,074 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:17:30,075 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-20_01-17-30.log] [testng] 01:17:30,075 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a6b121d - End of configuration. [testng] [2024-12-20 01:17:31,870] [pool-1-thread-10] Initializing /data/qa-2983/004007000.flex: [testng] 01:17:31,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:17:31,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:17:31,871 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-20_01-17-31.log] [testng] 01:17:31,871 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b4d7f3 - End of configuration. [testng] [2024-12-20 01:17:34,059] [pool-1-thread-9] Initializing /data/ghislain/test.flex: [testng] 01:17:34,059 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:17:34,059 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:17:34,060 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-20_01-17-34.log] [testng] 01:17:34,060 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2efec8b5 - End of configuration. [testng] [2024-12-20 01:17:35,948] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] 01:17:35,948 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:17:35,948 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:17:35,949 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-20_01-17-35.log] [testng] 01:17:35,949 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5066403c - End of configuration. [testng] [2024-12-20 01:17:50,958] [pool-1-thread-7] Initializing /data/tamjid/006004000.flex: [testng] 01:17:50,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:17:50,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:17:50,959 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-20_01-17-50.log] [testng] 01:17:50,959 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64a5ed7e - End of configuration. [testng] [2024-12-20 01:17:52,962] [pool-1-thread-6] Initializing /data/manuel/003003001.flex: [testng] 01:17:52,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:17:52,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:17:52,962 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-20_01-17-52.log] [testng] 01:17:52,963 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7bea6d25 - End of configuration. [testng] [2024-12-20 01:17:55,194] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] 01:17:55,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:17:55,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:17:55,195 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-20_01-17-55.log] [testng] 01:17:55,195 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7871f655 - End of configuration. [testng] [2024-12-20 01:18:11,229] [pool-1-thread-4] Initializing /data/tony/015002000.tiff: [testng] 01:18:11,229 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:18:11,229 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:18:11,230 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-20_01-18-11.log] [testng] 01:18:11,230 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c736e29 - End of configuration. [testng] [2024-12-20 01:18:15,465] [pool-1-thread-3] Initializing /data/tamjid/006005000.flex: [testng] 01:18:15,465 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:18:15,465 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:18:15,466 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-20_01-18-15.log] [testng] 01:18:15,466 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22dbfbcc - End of configuration. [testng] [2024-12-20 01:18:17,359] [pool-1-thread-2] Initializing /data/tony/003003000.tiff: [testng] 01:18:17,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:18:17,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:18:17,360 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-20_01-18-17.log] [testng] 01:18:17,360 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ca5fac8 - End of configuration. [testng] [2024-12-20 01:18:48,623] [pool-1-thread-4] Initializing /data/stephane/002007000.flex: [testng] [2024-12-20 01:18:50,230] [pool-1-thread-2] Initializing /data/qa-17190/002002011.flex: [testng] [2024-12-20 01:18:51,695] [pool-1-thread-7] Initializing /data/anatole/001004000.flex: [testng] [2024-12-20 01:18:53,176] [pool-1-thread-10] Initializing /data/tony/test1.flex: [testng] [2024-12-20 01:18:54,635] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [2024-12-20 01:19:08,241] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] [2024-12-20 01:19:12,677] [pool-1-thread-11] Initializing /data/tamjid/006003000.flex: [testng] [2024-12-20 01:19:26,878] [pool-1-thread-1] Initializing /data/tony/003008000.flex: [testng] [2024-12-20 01:19:33,489] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-12-20 01:19:35,821] [pool-1-thread-10] Initializing /data/tony/test.tiff: [testng] [2024-12-20 01:19:40,271] [pool-1-thread-4] Initializing /data/qa-18096/002002001.flex: [testng] [2024-12-20 01:19:42,173] [pool-1-thread-6] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-12-20 01:19:56,683] [pool-1-thread-11] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-12-20 01:20:06,642] [pool-1-thread-9] Initializing /data/tony/001014000 - from flex.tif: [testng] [2024-12-20 01:20:23,147] [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] [2024-12-20 01:20:25,352] [pool-1-thread-10] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-12-20 01:20:29,515] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] [2024-12-20 01:20:31,962] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2024-12-20 01:20:44,455] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] [2024-12-20 01:20:48,964] [pool-1-thread-7] Initializing /data/achim/003003000.flex: [testng] [2024-12-20 01:20:51,393] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2024-12-20 01:21:15,290] [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] [2024-12-20 01:21:17,741] [pool-1-thread-11] Initializing /data/qa-7469/002002.flex: [testng] [2024-12-20 01:21:33,567] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-12-20 01:21:50,308] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-12-20 01:22:07,850] [pool-1-thread-1] Initializing /data/qa-18096/002003001.flex: [testng] [2024-12-20 01:22:12,542] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-12-20 01:22:33,708] [pool-1-thread-11] Initializing /data/stephane/006013000.flex: [testng] [2024-12-20 01:22:40,142] [pool-1-thread-4] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-12-20 01:22:50,759] [pool-1-thread-1] Initializing /data/tony/001001000_objects.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 27 minutes 55 seconds Finished: SUCCESS