Started by upstream project "BIOFORMATS-test-repo" build number 204
originally caused by:
Started by upstream project "Trigger" build number 230
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3
[BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins6450613218665102619.sh
+ '[' flex = slidebook ']'
++ date +%u
+ '[' 7 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_32345_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] 01:49:33,274 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:49:33,276 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service.
[testng] 01:49:33,276 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:49:33,277 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:49:33,277 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:49:33,277 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:49:33,278 |-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] 01:49:33,278 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:49:33,278 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:49:33,279 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:49:33,279 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:49:33,279 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:49:33,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:49:33,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:49:33,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:49:33,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:49:33,485 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:49:33,485 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:49:33,485 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:49:33,485 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:49:33,485 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration.
[testng] 01:49:33,486 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point
[testng] 01:49:33,486 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 208 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-09-29 01:49:33,496] [main] java.version = 17.0.2
[testng] 01:49:33,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:49:33,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:49:33,541 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-29_01-49-33.log]
[testng] 01:49:33,543 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration.
[testng] [2024-09-29 01:49:33,545] [main] testng.directory = /data
[testng] [2024-09-29 01:49:33,545] [main] testng.configDirectory = /config
[testng] [2024-09-29 01:49:33,554] [main] testng.multiplier = 1.0
[testng] [2024-09-29 01:49:33,555] [main] testng.in-memory = false
[testng] [2024-09-29 01:49:33,555] [main] testng.allow-missing = false
[testng] [2024-09-29 01:49:33,555] [main] user.language = en
[testng] [2024-09-29 01:49:33,556] [main] user.country = ${user.country}
[testng] [2024-09-29 01:49:33,556] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-09-29 01:50:11,897] [main] ----------------------------------------
[testng] [2024-09-29 01:50:11,897] [main] Total files: 791
[testng] [2024-09-29 01:50:11,897] [main] Scan time: 38.341 s (48 ms/file)
[testng] [2024-09-29 01:50:11,897] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 42 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-09-29 01:55:13,839] [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] 01:55:13,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:55:13,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:55:13,840 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-29_01-55-13.log]
[testng] 01:55:13,841 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42bf2b01 - End of configuration.
[testng] [2024-09-29 01:55:14,587] [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] 01:55:14,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:55:14,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:55:14,588 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-29_01-55-14.log]
[testng] 01:55:14,589 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52bc526f - End of configuration.
[testng] [2024-09-29 01:55:15,069] [pool-1-thread-11] Initializing /data/tony/test.tiff:
[testng] 01:55:15,069 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:55:15,069 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:55:15,070 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-29_01-55-15.log]
[testng] 01:55:15,070 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b3adad1 - End of configuration.
[testng] [2024-09-29 01:55:18,338] [pool-1-thread-10] Initializing /data/tony/003008000.flex:
[testng] 01:55:18,338 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:55:18,338 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:55:18,339 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-29_01-55-18.log]
[testng] 01:55:18,339 |-INFO in ch.qos.logback.core.sift.SiftProcessor@16555ee4 - End of configuration.
[testng] [2024-09-29 01:55:18,764] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex:
[testng] 01:55:18,764 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:55:18,764 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:55:18,765 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-29_01-55-18.log]
[testng] 01:55:18,765 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ef87e45 - End of configuration.
[testng] [2024-09-29 01:55:19,196] [pool-1-thread-8] Initializing /data/tony/000101400 - from PE sofwatre.tif:
[testng] 01:55:19,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:55:19,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:55:19,197 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-29_01-55-19.log]
[testng] 01:55:19,198 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ae25506 - End of configuration.
[testng] [2024-09-29 01:55:20,108] [pool-1-thread-7] Initializing /data/qa-18096/002002001.flex:
[testng] 01:55:20,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:55:20,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:55:20,108 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-29_01-55-20.log]
[testng] 01:55:20,109 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d632233 - End of configuration.
[testng] [2024-09-29 01:55:20,536] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex:
[testng] 01:55:20,536 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:55:20,536 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:55:20,537 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-29_01-55-20.log]
[testng] 01:55:20,537 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f82be93 - End of configuration.
[testng] [2024-09-29 01:55:23,637] [pool-1-thread-5] Initializing /data/stephane/002007000.flex:
[testng] 01:55:23,637 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:55:23,637 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:55:23,638 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-29_01-55-23.log]
[testng] 01:55:23,638 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6477d1f3 - End of configuration.
[testng] [2024-09-29 01:55:24,142] [pool-1-thread-4] Initializing /data/tony/015002000.tiff:
[testng] 01:55:24,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:55:24,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:55:24,143 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-29_01-55-24.log]
[testng] 01:55:24,144 |-INFO in ch.qos.logback.core.sift.SiftProcessor@692d5e0b - End of configuration.
[testng] [2024-09-29 01:55:24,973] [pool-1-thread-3] Initializing /data/qa-17190/002002011.flex:
[testng] 01:55:24,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:55:24,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:55:24,974 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-29_01-55-24.log]
[testng] 01:55:24,974 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28afa215 - End of configuration.
[testng] [2024-09-29 01:55:25,352] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex:
[testng] 01:55:25,352 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:55:25,352 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:55:25,352 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-29_01-55-25.log]
[testng] 01:55:25,353 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a284b4e - End of configuration.
[testng] [2024-09-29 01:55:35,840] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex:
[testng] [2024-09-29 01:55:40,483] [pool-1-thread-4] Initializing /data/tamjid/006005000.flex:
[testng] [2024-09-29 01:55:40,962] [pool-1-thread-11] Initializing /data/stephane/006013000.flex:
[testng] [2024-09-29 01:55:41,472] [pool-1-thread-3] Initializing /data/manuel/003003001.flex:
[testng] [2024-09-29 01:55:42,053] [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] [2024-09-29 01:55:43,004] [pool-1-thread-5] Initializing /data/tamjid/006003000.flex:
[testng] [2024-09-29 01:55:47,182] [pool-1-thread-10] Initializing /data/qa-2983/004007000.flex:
[testng] [2024-09-29 01:55:47,755] [pool-1-thread-9] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex:
[testng] [2024-09-29 01:55:48,317] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex:
[testng] [2024-09-29 01:55:55,494] [pool-1-thread-4] Initializing /data/tony/003003000.tiff:
[testng] [2024-09-29 01:55:56,838] [pool-1-thread-5] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex:
[testng] [2024-09-29 01:55:58,118] [pool-1-thread-1] Initializing /data/tony/001001000_objects.flex:
[testng] [2024-09-29 01:56:01,874] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex:
[testng] [2024-09-29 01:56:02,561] [pool-1-thread-3] Initializing /data/qa-7469/002002.flex:
[testng] [2024-09-29 01:56:03,146] [pool-1-thread-11] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex:
[testng] [2024-09-29 01:56:04,015] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex:
[testng] [2024-09-29 01:56:06,462] [pool-1-thread-4] Initializing /data/achim/003003000.flex:
[testng] [2024-09-29 01:56:08,192] [pool-1-thread-1] Initializing /data/public/idr0007/Plate1/001001000.flex:
[testng] [2024-09-29 01:56:16,365] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex:
[testng] [2024-09-29 01:56:19,480] [pool-1-thread-10] Initializing /data/tamjid/006004000.flex:
[testng] [2024-09-29 01:56:20,598] [pool-1-thread-7] Initializing /data/tony/001014000 - from flex.tif:
[testng] [2024-09-29 01:56:21,978] [pool-1-thread-9] Initializing /data/ghislain/test.flex:
[testng] [2024-09-29 01:56:22,868] [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] [2024-09-29 01:56:27,943] [pool-1-thread-10] Initializing /data/anatole/001004000.flex:
[testng] [2024-09-29 01:56:30,963] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex:
[testng] [2024-09-29 01:56:31,546] [pool-1-thread-3] Initializing /data/tony/test1.flex:
[testng] [2024-09-29 01:56:33,229] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex:
[testng] [2024-09-29 01:56:39,850] [pool-1-thread-3] Initializing /data/qa-18096/002003001.flex:
[testng] [2024-09-29 01:56:44,338] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex:
[testng] [2024-09-29 01:56:50,658] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 2226, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 13 minutes 23 seconds
Finished: SUCCESS