Started by upstream project "BIOFORMATS-test-repo" build number 201
originally caused by:
Started by upstream project "Trigger" build number 226
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/jenkins11146313962707736907.sh
+ '[' specs = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_31823_merge_ci -v /uod/idr/repos/curated/specs:/data -v /uod/idr-scratch/merge-ci/curated/specs:/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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release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] 12:15:44,919 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 12:15:44,920 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service.
[testng] 12:15:44,920 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 12:15:44,921 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 12:15:44,921 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 12:15:44,922 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 12:15:44,922 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 12:15:44,922 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 12:15:44,922 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 12:15:44,923 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 12:15:44,923 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 12:15:44,923 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 12:15:45,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 12:15:45,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 12:15:45,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 12:15:45,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 12:15:45,119 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 12:15:45,119 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 12:15:45,120 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 12:15:45,120 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 12:15:45,120 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration.
[testng] 12:15:45,121 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point
[testng] 12:15:45,121 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 199 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-09-26 12:15:45,130] [main] java.version = 21
[testng] 12:15:45,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 12:15:45,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:15:45,184 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-26_12-15-45.log]
[testng] 12:15:45,186 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration.
[testng] [2024-09-26 12:15:45,188] [main] testng.directory = /data
[testng] [2024-09-26 12:15:45,188] [main] testng.configDirectory = /config
[testng] [2024-09-26 12:15:45,196] [main] testng.multiplier = 1.0
[testng] [2024-09-26 12:15:45,197] [main] testng.in-memory = false
[testng] [2024-09-26 12:15:45,197] [main] testng.allow-missing = false
[testng] [2024-09-26 12:15:45,197] [main] user.language = en
[testng] [2024-09-26 12:15:45,197] [main] user.country = ${user.country}
[testng] [2024-09-26 12:15:45,197] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-09-26 12:18:16,562] [main] ----------------------------------------
[testng] [2024-09-26 12:18:16,562] [main] Total files: 226
[testng] [2024-09-26 12:18:16,562] [main] Scan time: 151.365 s (669 ms/file)
[testng] [2024-09-26 12:18:16,563] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 28 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-09-26 12:19:27,414] [pool-1-thread-1] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/Test2.dm3:
[testng] 12:19:27,414 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 12:19:27,414 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:19:27,416 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-26_12-19-27.log]
[testng] 12:19:27,416 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53e97f8d - End of configuration.
[testng] [2024-09-26 12:19:27,473] [pool-1-thread-12] Initializing /data/fluoview/sample_labled_XYZTCh.tif:
[testng] 12:19:27,473 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 12:19:27,473 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:19:27,474 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-26_12-19-27.log]
[testng] 12:19:27,475 |-INFO in ch.qos.logback.core.sift.SiftProcessor@870a299 - End of configuration.
[testng] [2024-09-26 12:19:27,638] [pool-1-thread-11] Initializing /data/iplab/Color Image.IPL:
[testng] 12:19:27,638 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 12:19:27,638 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:19:27,639 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-26_12-19-27.log]
[testng] 12:19:27,640 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a002f1 - End of configuration.
[testng] [2024-09-26 12:19:27,669] [pool-1-thread-10] Initializing /data/fluoview/sample_labled_XYZCh.tif:
[testng] 12:19:27,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 12:19:27,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:19:27,671 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-26_12-19-27.log]
[testng] 12:19:27,672 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64b7ea9 - End of configuration.
[testng] [2024-09-26 12:19:27,843] [pool-1-thread-9] Initializing /data/iplab/Blend_Dapi.IPL:
[testng] 12:19:27,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 12:19:27,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:19:27,844 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-26_12-19-27.log]
[testng] 12:19:27,845 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2fdc1a62 - End of configuration.
[testng] [2024-09-26 12:19:27,872] [pool-1-thread-8] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/Test.dm3:
[testng] 12:19:27,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 12:19:27,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:19:27,873 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-26_12-19-27.log]
[testng] 12:19:27,873 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68b25825 - End of configuration.
[testng] [2024-09-26 12:19:27,915] [pool-1-thread-7] Initializing /data/fluoview/Sample_TwoCH.TIF:
[testng] 12:19:27,916 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 12:19:27,916 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:19:27,917 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-26_12-19-27.log]
[testng] 12:19:27,917 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67fbeca0 - End of configuration.
[testng] [2024-09-26 12:19:28,089] [pool-1-thread-6] Initializing /data/iplab/Color Histology.IPL:
[testng] 12:19:28,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 12:19:28,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:19:28,090 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-26_12-19-28.log]
[testng] 12:19:28,090 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10221a1d - End of configuration.
[testng] [2024-09-26 12:19:28,120] [pool-1-thread-5] Initializing /data/iplab/Blend_Tritc.IPL:
[testng] 12:19:28,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 12:19:28,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:19:28,122 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-26_12-19-28.log]
[testng] 12:19:28,123 |-INFO in ch.qos.logback.core.sift.SiftProcessor@511e2292 - End of configuration.
[testng] [2024-09-26 12:19:28,150] [pool-1-thread-4] Initializing /data/fluoview/Sample_XT.tif:
[testng] 12:19:28,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 12:19:28,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:19:28,152 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-26_12-19-28.log]
[testng] 12:19:28,152 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54bd2649 - End of configuration.
[testng] [2024-09-26 12:19:28,307] [pool-1-thread-3] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/test3.dm3:
[testng] 12:19:28,307 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 12:19:28,307 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:19:28,308 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-26_12-19-28.log]
[testng] 12:19:28,308 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e9ab45e - End of configuration.
[testng] [2024-09-26 12:19:28,344] [pool-1-thread-2] Initializing /data/fluoview/Sample_ThreeCH.TIF:
[testng] 12:19:28,344 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 12:19:28,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:19:28,345 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-26_12-19-28.log]
[testng] 12:19:28,346 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f690185 - End of configuration.
[testng] [2024-09-26 12:19:30,519] [pool-1-thread-6] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile-2.lsm:
[testng] [2024-09-26 12:19:30,850] [pool-1-thread-11] Initializing /data/fluoview/SpineAnimation.tif:
[testng] [2024-09-26 12:19:31,032] [pool-1-thread-3] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile--MultiTrack-1.lsm:
[testng] [2024-09-26 12:19:31,270] [pool-1-thread-8] Initializing /data/fluoview/SpineAnimation.avi:
[testng] [2024-09-26 12:19:31,367] [pool-1-thread-1] Initializing /data/fluoview/sample_labled_XYTCh.tif:
[testng] [2024-09-26 12:19:31,704] [pool-1-thread-5] Initializing /data/fluoview/Sample_XYT.TIF:
[testng] [2024-09-26 12:19:31,878] [pool-1-thread-9] Initializing /data/iplab/Actin.IPL:
[testng] [2024-09-26 12:19:32,163] [pool-1-thread-10] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile-1.lsm:
[testng] [2024-09-26 12:19:32,397] [pool-1-thread-12] Initializing /data/fluoview/Sample_XYZ.TIF:
[testng] [2024-09-26 12:19:33,045] [pool-1-thread-7] Initializing /data/iplab/Blend_Final.IPL:
[testng] [2024-09-26 12:19:33,097] [pool-1-thread-4] Initializing /data/iplab/Blend_DIC.IPL:
[testng] [2024-09-26 12:19:33,148] [pool-1-thread-2] Initializing /data/iplab/10x Blood and Bacteria.IPL:
[testng] [2024-09-26 12:19:33,207] [pool-1-thread-9] Initializing /data/iplab/Chromosomes.IPL:
[testng] [2024-09-26 12:19:33,573] [pool-1-thread-8] Initializing /data/iplab/16Bit XRay.IPL:
[testng] [2024-09-26 12:19:33,998] [pool-1-thread-9] Initializing /data/iplab/Blend_Fitc.IPL:
[testng] [2024-09-26 12:19:34,075] [pool-1-thread-7] Initializing /data/iplab/3t3 Cell.IPL:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1484, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 3 minutes 55 seconds
Finished: SUCCESS