Started by upstream project "BIOFORMATS-test-repo" build number 72
originally caused by:
Started by upstream project "Trigger" build number 80
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4
[BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins15457714719242766689.sh
+ '[' imaris = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_10914_merge_ci -v /uod/idr/repos/curated/imaris:/data -v /uod/idr-scratch/merge-ci/curated/imaris:/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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release
[javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
[javac] 4 warnings
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] 02:15:34,236 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 02:15:34,238 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service.
[testng] 02:15:34,238 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:15:34,240 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:15:34,241 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 02:15:34,241 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 02:15:34,242 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 02:15:34,242 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:15:34,242 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:15:34,243 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 02:15:34,244 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 02:15:34,244 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 02:15:34,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 02:15:34,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 02:15:34,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 02:15:34,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 02:15:34,488 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 02:15:34,488 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 02:15:34,489 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 02:15:34,489 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 02:15:34,490 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration.
[testng] 02:15:34,491 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point
[testng] 02:15:34,491 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 249 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-05-23 02:15:34,506] [main] java.version = 21
[testng] 02:15:34,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 02:15:34,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:15:34,579 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-23_02-15-34.log]
[testng] 02:15:34,581 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration.
[testng] [2024-05-23 02:15:34,584] [main] testng.directory = /data
[testng] [2024-05-23 02:15:34,584] [main] testng.configDirectory = /config
[testng] [2024-05-23 02:15:34,595] [main] testng.multiplier = 1.0
[testng] [2024-05-23 02:15:34,596] [main] testng.in-memory = false
[testng] [2024-05-23 02:15:34,596] [main] testng.allow-missing = false
[testng] [2024-05-23 02:15:34,596] [main] user.language = en
[testng] [2024-05-23 02:15:34,596] [main] user.country = ${user.country}
[testng] [2024-05-23 02:15:34,596] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-05-23 02:15:41,248] [main] ----------------------------------------
[testng] [2024-05-23 02:15:41,248] [main] Total files: 67
[testng] [2024-05-23 02:15:41,248] [main] Scan time: 6.651 s (99 ms/file)
[testng] [2024-05-23 02:15:41,248] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 59 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-05-23 02:16:02,833] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0006.ims:
[testng] 02:16:02,834 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:16:02,834 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:16:02,836 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-23_02-16-02.log]
[testng] 02:16:02,836 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a87792 - End of configuration.
[testng] [2024-05-23 02:16:02,859] [pool-1-thread-12] Initializing /data/public/davemason/Convallaria_3C_3T_2x2grid_confocal.ims:
[testng] 02:16:02,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:16:02,860 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:16:02,860 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-23_02-16-02.log]
[testng] 02:16:02,861 |-INFO in ch.qos.logback.core.sift.SiftProcessor@633132f5 - End of configuration.
[testng] [2024-05-23 02:16:02,905] [pool-1-thread-11] Initializing /data/jason/imaris_5_5_demoimages/SwimmingAlgae.ims:
[testng] 02:16:02,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:16:02,906 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:16:02,906 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-23_02-16-02.log]
[testng] 02:16:02,907 |-INFO in ch.qos.logback.core.sift.SiftProcessor@308cd3e3 - End of configuration.
[testng] [2024-05-23 02:16:02,965] [pool-1-thread-10] Initializing /data/generated/MF-2CH-Z-T.ims:
[testng] 02:16:02,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:16:02,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:16:02,966 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-23_02-16-02.log]
[testng] 02:16:02,966 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e114881 - End of configuration.
[testng] [2024-05-23 02:16:02,981] [pool-1-thread-9] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal_deconvolved.ims:
[testng] 02:16:02,982 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:16:02,982 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:16:02,983 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-23_02-16-02.log]
[testng] 02:16:02,983 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e715bec - End of configuration.
[testng] [2024-05-23 02:16:03,023] [pool-1-thread-8] Initializing /data/generated/10-31_E_t0013.ims:
[testng] 02:16:03,023 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:16:03,023 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:16:03,024 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-23_02-16-03.log]
[testng] 02:16:03,025 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23ac65bc - End of configuration.
[testng] [2024-05-23 02:16:03,040] [pool-1-thread-7] Initializing /data/qa-17839/Fusion _Stack.ims:
[testng] 02:16:03,040 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:16:03,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:16:03,042 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-23_02-16-03.log]
[testng] 02:16:03,042 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39e28d0f - End of configuration.
[testng] [2024-05-23 02:16:03,102] [pool-1-thread-6] Initializing /data/public/eliana/retina_large.ims:
[testng] 02:16:03,102 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:16:03,102 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:16:03,103 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-23_02-16-03.log]
[testng] 02:16:03,104 |-INFO in ch.qos.logback.core.sift.SiftProcessor@bf95aef - End of configuration.
[testng] [2024-05-23 02:16:03,131] [pool-1-thread-5] Initializing /data/jason/imaris_5_5_demoimages/PtK2Cell.ims:
[testng] 02:16:03,131 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:16:03,132 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:16:03,133 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-23_02-16-03.log]
[testng] 02:16:03,133 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2eb8dac2 - End of configuration.
[testng] [2024-05-23 02:16:03,163] [pool-1-thread-4] Initializing /data/generated/10-31_E_t0010.ims:
[testng] 02:16:03,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:16:03,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:16:03,164 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-23_02-16-03.log]
[testng] 02:16:03,164 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ce32a39 - End of configuration.
[testng] [2024-05-23 02:16:03,176] [pool-1-thread-3] Initializing /data/generated/10-31_E_t0014.ims:
[testng] 02:16:03,176 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:16:03,176 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:16:03,177 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-23_02-16-03.log]
[testng] 02:16:03,177 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65c478e6 - End of configuration.
[testng] [2024-05-23 02:16:03,189] [pool-1-thread-2] Initializing /data/qa-17515/Organoid=1.ims:
[testng] 02:16:03,189 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:16:03,189 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:16:03,190 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-23_02-16-03.log]
[testng] 02:16:03,190 |-INFO in ch.qos.logback.core.sift.SiftProcessor@355e645c - End of configuration.
BUILD SUCCESSFUL
Total time: 1 minute 30 seconds
Finished: SUCCESS