Started by upstream project "BIOFORMATS-test-repo" build number 249
originally caused by:
Started by upstream project "Trigger" build number 273
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/jenkins8628636375337398785.sh
+ '[' specs = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_39179_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
test-automated:
[testng] File leak detector installed
[testng] 00:31:31,165 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 00:31:31,167 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service.
[testng] 00:31:31,167 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:31:31,168 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:31:31,168 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 00:31:31,169 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 00:31:31,169 |-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] 00:31:31,169 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:31:31,169 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:31:31,170 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 00:31:31,170 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 00:31:31,170 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 00:31:31,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 00:31:31,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 00:31:31,419 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 00:31:31,419 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 00:31:31,427 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 00:31:31,427 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 00:31:31,427 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 00:31:31,427 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 00:31:31,427 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration.
[testng] 00:31:31,428 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point
[testng] 00:31:31,428 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 259 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-11-08 00:31:31,438] [main] java.version = 1.8.0_342
[testng] 00:31:31,441 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 00:31:31,441 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:31:31,486 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-08_00-31-31.log]
[testng] 00:31:31,488 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration.
[testng] [2024-11-08 00:31:31,490] [main] testng.directory = /data
[testng] [2024-11-08 00:31:31,490] [main] testng.configDirectory = /config
[testng] [2024-11-08 00:31:31,502] [main] testng.multiplier = 1.0
[testng] [2024-11-08 00:31:31,502] [main] testng.in-memory = false
[testng] [2024-11-08 00:31:31,502] [main] testng.allow-missing = false
[testng] [2024-11-08 00:31:31,502] [main] user.language = en
[testng] [2024-11-08 00:31:31,502] [main] user.country = ${user.country}
[testng] [2024-11-08 00:31:31,502] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-11-08 00:35:52,272] [main] ----------------------------------------
[testng] [2024-11-08 00:35:52,273] [main] Total files: 226
[testng] [2024-11-08 00:35:52,273] [main] Scan time: 260.769 s (1153 ms/file)
[testng] [2024-11-08 00:35:52,273] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 28 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-11-08 00:37:54,717] [pool-1-thread-1] Initializing /data/iplab/Blend_Fitc.IPL:
[testng] 00:37:54,717 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 00:37:54,717 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:37:54,718 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-08_00-37-54.log]
[testng] 00:37:54,718 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5fcf5d32 - End of configuration.
[testng] [2024-11-08 00:37:54,843] [pool-1-thread-12] Initializing /data/fluoview/sample_labled_XYZTCh.tif:
[testng] 00:37:54,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 00:37:54,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:37:54,845 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-08_00-37-54.log]
[testng] 00:37:54,845 |-INFO in ch.qos.logback.core.sift.SiftProcessor@92b9339 - End of configuration.
[testng] [2024-11-08 00:37:55,336] [pool-1-thread-11] Initializing /data/fluoview/Sample_XT.tif:
[testng] 00:37:55,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 00:37:55,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:37:55,337 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-08_00-37-55.log]
[testng] 00:37:55,337 |-INFO in ch.qos.logback.core.sift.SiftProcessor@360e4396 - End of configuration.
[testng] [2024-11-08 00:37:56,088] [pool-1-thread-10] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/test3.dm3:
[testng] 00:37:56,088 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 00:37:56,088 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:37:56,089 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-08_00-37-56.log]
[testng] 00:37:56,090 |-INFO in ch.qos.logback.core.sift.SiftProcessor@414f0263 - End of configuration.
[testng] [2024-11-08 00:37:56,221] [pool-1-thread-9] Initializing /data/fluoview/Sample_ThreeCH.TIF:
[testng] 00:37:56,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 00:37:56,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:37:56,221 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-08_00-37-56.log]
[testng] 00:37:56,222 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4564587d - End of configuration.
[testng] [2024-11-08 00:37:56,811] [pool-1-thread-8] Initializing /data/fluoview/sample_labled_XYZCh.tif:
[testng] 00:37:56,811 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 00:37:56,812 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:37:56,812 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-08_00-37-56.log]
[testng] 00:37:56,812 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ba38109 - End of configuration.
[testng] [2024-11-08 00:37:57,498] [pool-1-thread-7] Initializing /data/iplab/Blend_Final.IPL:
[testng] 00:37:57,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 00:37:57,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:37:57,499 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-08_00-37-57.log]
[testng] 00:37:57,500 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1bbeb850 - End of configuration.
[testng] [2024-11-08 00:37:57,585] [pool-1-thread-6] Initializing /data/fluoview/Sample_XYT.TIF:
[testng] 00:37:57,586 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 00:37:57,586 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:37:57,586 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-08_00-37-57.log]
[testng] 00:37:57,586 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a93fbee - End of configuration.
[testng] [2024-11-08 00:37:58,431] [pool-1-thread-5] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/Test2.dm3:
[testng] 00:37:58,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 00:37:58,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:37:58,431 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-08_00-37-58.log]
[testng] 00:37:58,432 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45aefea2 - End of configuration.
[testng] [2024-11-08 00:37:58,601] [pool-1-thread-4] Initializing /data/iplab/10x Blood and Bacteria.IPL:
[testng] 00:37:58,602 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 00:37:58,602 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:37:58,602 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-08_00-37-58.log]
[testng] 00:37:58,603 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53c53f02 - End of configuration.
[testng] [2024-11-08 00:37:58,736] [pool-1-thread-3] Initializing /data/fluoview/Sample_XYZ.TIF:
[testng] 00:37:58,736 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 00:37:58,736 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:37:58,737 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-08_00-37-58.log]
[testng] 00:37:58,737 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18aa4327 - End of configuration.
[testng] [2024-11-08 00:37:59,958] [pool-1-thread-2] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile--MultiTrack-1.lsm:
[testng] 00:37:59,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 00:37:59,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:37:59,959 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-08_00-37-59.log]
[testng] 00:37:59,960 |-INFO in ch.qos.logback.core.sift.SiftProcessor@145f9a40 - End of configuration.
[testng] [2024-11-08 00:38:05,211] [pool-1-thread-7] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile-2.lsm:
[testng] [2024-11-08 00:38:05,903] [pool-1-thread-4] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/Test.dm3:
[testng] [2024-11-08 00:38:06,086] [pool-1-thread-1] Initializing /data/iplab/Blend_Tritc.IPL:
[testng] [2024-11-08 00:38:06,200] [pool-1-thread-5] Initializing /data/fluoview/Sample_TwoCH.TIF:
[testng] [2024-11-08 00:38:06,742] [pool-1-thread-10] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile-1.lsm:
[testng] [2024-11-08 00:38:10,507] [pool-1-thread-1] Initializing /data/fluoview/SpineAnimation.avi:
[testng] [2024-11-08 00:38:11,154] [pool-1-thread-4] Initializing /data/iplab/Blend_Dapi.IPL:
[testng] [2024-11-08 00:38:11,885] [pool-1-thread-12] Initializing /data/iplab/Chromosomes.IPL:
[testng] [2024-11-08 00:38:12,057] [pool-1-thread-3] Initializing /data/iplab/Actin.IPL:
[testng] [2024-11-08 00:38:12,200] [pool-1-thread-8] Initializing /data/fluoview/SpineAnimation.tif:
[testng] [2024-11-08 00:38:12,858] [pool-1-thread-6] Initializing /data/iplab/Color Histology.IPL:
[testng] [2024-11-08 00:38:12,936] [pool-1-thread-9] Initializing /data/fluoview/sample_labled_XYTCh.tif:
[testng] [2024-11-08 00:38:13,506] [pool-1-thread-11] Initializing /data/iplab/3t3 Cell.IPL:
[testng] [2024-11-08 00:38:14,807] [pool-1-thread-4] Initializing /data/iplab/Blend_DIC.IPL:
[testng] [2024-11-08 00:38:15,988] [pool-1-thread-1] Initializing /data/iplab/Color Image.IPL:
[testng] [2024-11-08 00:38:16,397] [pool-1-thread-12] Initializing /data/iplab/16Bit XRay.IPL:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1484, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 6 minutes 54 seconds
Finished: SUCCESS