Started by upstream project "BIOFORMATS-test-repo" build number 273
originally caused by:
Started by user devspace
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9
[BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins7580372204705574295.sh
+ '[' flex = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_43016_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] 07:41:51,463 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 07:41:51,465 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service.
[testng] 07:41:51,465 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 07:41:51,466 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 07:41:51,466 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 07:41:51,466 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 07:41:51,466 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 07:41:51,466 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 07:41:51,467 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 07:41:51,467 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 07:41:51,467 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 07:41:51,467 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 07:41:51,681 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 07:41:51,681 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 07:41:51,707 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 07:41:51,707 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 07:41:51,714 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 07:41:51,714 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 07:41:51,715 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 07:41:51,715 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 07:41:51,715 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration.
[testng] 07:41:51,716 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point
[testng] 07:41:51,716 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 249 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-11-29 07:41:51,725] [main] java.version = 1.8.0_342
[testng] 07:41:51,728 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 07:41:51,728 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 07:41:51,771 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-29_07-41-51.log]
[testng] 07:41:51,773 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration.
[testng] [2024-11-29 07:41:51,775] [main] testng.directory = /data
[testng] [2024-11-29 07:41:51,775] [main] testng.configDirectory = /config
[testng] [2024-11-29 07:41:51,786] [main] testng.multiplier = 1.0
[testng] [2024-11-29 07:41:51,787] [main] testng.in-memory = false
[testng] [2024-11-29 07:41:51,787] [main] testng.allow-missing = false
[testng] [2024-11-29 07:41:51,787] [main] user.language = en
[testng] [2024-11-29 07:41:51,787] [main] user.country = ${user.country}
[testng] [2024-11-29 07:41:51,787] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-11-29 07:44:06,399] [main] ----------------------------------------
[testng] [2024-11-29 07:44:06,399] [main] Total files: 791
[testng] [2024-11-29 07:44:06,400] [main] Scan time: 134.612 s (170 ms/file)
[testng] [2024-11-29 07:44:06,400] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 42 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-11-29 07:51:56,145] [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] 07:51:56,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 07:51:56,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 07:51:56,147 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-29_07-51-56.log]
[testng] 07:51:56,148 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2abb421a - End of configuration.
[testng] [2024-11-29 07:51:58,339] [pool-1-thread-12] Initializing /data/tamjid/006004000.flex:
[testng] 07:51:58,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 07:51:58,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 07:51:58,340 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-29_07-51-58.log]
[testng] 07:51:58,340 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ef665b1 - End of configuration.
[testng] [2024-11-29 07:51:59,916] [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] 07:51:59,916 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 07:51:59,916 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 07:51:59,917 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-29_07-51-59.log]
[testng] 07:51:59,918 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f416a94 - End of configuration.
[testng] [2024-11-29 07:52:04,099] [pool-1-thread-10] Initializing /data/manuel/003003001.flex:
[testng] 07:52:04,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 07:52:04,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 07:52:04,101 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-29_07-52-04.log]
[testng] 07:52:04,101 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10828724 - End of configuration.
[testng] [2024-11-29 07:52:06,767] [pool-1-thread-9] Initializing /data/stephane/006013000.flex:
[testng] 07:52:06,767 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 07:52:06,767 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 07:52:06,768 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-29_07-52-06.log]
[testng] 07:52:06,768 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dd892e8 - End of configuration.
[testng] [2024-11-29 07:52:08,418] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex:
[testng] 07:52:08,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 07:52:08,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 07:52:08,419 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-29_07-52-08.log]
[testng] 07:52:08,419 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c0b0465 - End of configuration.
[testng] [2024-11-29 07:52:10,269] [pool-1-thread-7] Initializing /data/qa-17190/002002011.flex:
[testng] 07:52:10,270 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 07:52:10,270 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 07:52:10,270 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-29_07-52-10.log]
[testng] 07:52:10,271 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42e829aa - End of configuration.
[testng] [2024-11-29 07:52:12,011] [pool-1-thread-6] Initializing /data/tony/001001000_objects.flex:
[testng] 07:52:12,011 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 07:52:12,011 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 07:52:12,011 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-29_07-52-12.log]
[testng] 07:52:12,012 |-INFO in ch.qos.logback.core.sift.SiftProcessor@732b2eff - End of configuration.
[testng] [2024-11-29 07:52:13,741] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex:
[testng] 07:52:13,741 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 07:52:13,742 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 07:52:13,742 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-29_07-52-13.log]
[testng] 07:52:13,743 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6725ca8c - End of configuration.
[testng] [2024-11-29 07:52:27,378] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex:
[testng] 07:52:27,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 07:52:27,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 07:52:27,378 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-29_07-52-27.log]
[testng] 07:52:27,379 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e9c2fd0 - End of configuration.
[testng] [2024-11-29 07:52:42,897] [pool-1-thread-3] Initializing /data/tony/001014000 - from flex.tif:
[testng] 07:52:42,897 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 07:52:42,897 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 07:52:42,898 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-29_07-52-42.log]
[testng] 07:52:42,898 |-INFO in ch.qos.logback.core.sift.SiftProcessor@437ce5a9 - End of configuration.
[testng] [2024-11-29 07:52:48,754] [pool-1-thread-2] Initializing /data/tony/test.tiff:
[testng] 07:52:48,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 07:52:48,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 07:52:48,755 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-29_07-52-48.log]
[testng] 07:52:48,755 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58aa4218 - End of configuration.
[testng] [2024-11-29 07:53:17,217] [pool-1-thread-3] Initializing /data/qa-2983/004007000.flex:
[testng] [2024-11-29 07:53:19,250] [pool-1-thread-2] Initializing /data/public/idr0007/Plate1/001001000.flex:
[testng] [2024-11-29 07:53:32,137] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex:
[testng] [2024-11-29 07:53:34,875] [pool-1-thread-7] Initializing /data/ghislain/test.flex:
[testng] [2024-11-29 07:53:36,719] [pool-1-thread-6] Initializing /data/tony/000101400 - from PE sofwatre.tif:
[testng] [2024-11-29 07:53:49,769] [pool-1-thread-1] Initializing /data/tony/test1.flex:
[testng] [2024-11-29 07:53:51,867] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex:
[testng] [2024-11-29 07:53:53,861] [pool-1-thread-9] Initializing /data/qa-7469/002002.flex:
[testng] [2024-11-29 07:53:55,718] [pool-1-thread-11] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex:
[testng] [2024-11-29 07:54:08,717] [pool-1-thread-6] Initializing /data/achim/003003000.flex:
[testng] [2024-11-29 07:54:10,838] [pool-1-thread-10] Initializing /data/qa-18096/002003001.flex:
[testng] [2024-11-29 07:54:12,891] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex:
[testng] [2024-11-29 07:54:31,382] [pool-1-thread-7] Initializing /data/tony/015002000.tiff:
[testng] [2024-11-29 07:54:48,302] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex:
[testng] [2024-11-29 07:54:50,901] [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] [2024-11-29 07:54:56,067] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex:
[testng] [2024-11-29 07:55:03,745] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex:
[testng] [2024-11-29 07:55:06,225] [pool-1-thread-10] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex:
[testng] [2024-11-29 07:55:17,505] [pool-1-thread-6] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex:
[testng] [2024-11-29 07:55:30,714] [pool-1-thread-9] Initializing /data/anatole/001004000.flex:
[testng] [2024-11-29 07:55:33,733] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex:
[testng] [2024-11-29 07:55:38,407] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex:
[testng] [2024-11-29 07:55:59,862] [pool-1-thread-12] Initializing /data/tamjid/006003000.flex:
[testng] [2024-11-29 07:56:05,055] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex:
[testng] [2024-11-29 07:56:32,592] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex:
[testng] [2024-11-29 07:56:52,997] [pool-1-thread-1] Initializing /data/stephane/002007000.flex:
[testng] [2024-11-29 07:56:59,891] [pool-1-thread-12] Initializing /data/qa-18096/002002001.flex:
[testng] [2024-11-29 07:57:12,351] [pool-1-thread-9] Initializing /data/tamjid/006005000.flex:
[testng] [2024-11-29 07:57:21,361] [pool-1-thread-11] Initializing /data/tony/003003000.tiff:
[testng] [2024-11-29 07:57:25,851] [pool-1-thread-1] Initializing /data/tony/003008000.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 42 seconds
Finished: SUCCESS