Started by upstream project "BIOFORMATS-test-repo" build number 191
originally caused by:
Started by upstream project "Trigger" build number 213
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/jenkins17528678863641154059.sh
+ '[' specs = slidebook ']'
++ date +%u
+ '[' 2 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_30183_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] 1 warning
test-automated:
[testng] WARNING: An illegal reflective access operation has occurred
[testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket
[testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener
[testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
[testng] WARNING: All illegal access operations will be denied in a future release
[testng] File leak detector installed
[testng] 01:27:26,624 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:27:26,625 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service.
[testng] 01:27:26,625 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:27:26,626 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:27:26,627 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:27:26,627 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:27:26,627 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:27:26,627 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:27:26,628 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:27:26,629 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:27:26,629 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:27:26,629 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:27:26,821 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:27:26,821 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:27:26,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:27:26,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:27:26,852 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:27:26,853 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:27:26,853 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:27:26,853 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:27:26,853 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration.
[testng] 01:27:26,854 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point
[testng] 01:27:26,854 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 226 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-09-17 01:27:26,864] [main] java.version = 11.0.16
[testng] 01:27:26,867 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:27:26,867 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:26,912 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-17_01-27-26.log]
[testng] 01:27:26,913 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
[testng] [2024-09-17 01:27:26,915] [main] testng.directory = /data
[testng] [2024-09-17 01:27:26,916] [main] testng.configDirectory = /config
[testng] [2024-09-17 01:27:26,926] [main] testng.multiplier = 1.0
[testng] [2024-09-17 01:27:26,927] [main] testng.in-memory = false
[testng] [2024-09-17 01:27:26,928] [main] testng.allow-missing = false
[testng] [2024-09-17 01:27:26,928] [main] user.language = en
[testng] [2024-09-17 01:27:26,928] [main] user.country = ${user.country}
[testng] [2024-09-17 01:27:26,928] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-09-17 01:27:46,919] [main] ----------------------------------------
[testng] [2024-09-17 01:27:46,920] [main] Total files: 226
[testng] [2024-09-17 01:27:46,920] [main] Scan time: 19.991 s (88 ms/file)
[testng] [2024-09-17 01:27:46,920] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 28 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-09-17 01:27:57,771] [pool-1-thread-1] Initializing /data/fluoview/Sample_ThreeCH.TIF:
[testng] 01:27:57,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:27:57,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:57,773 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-17_01-27-57.log]
[testng] 01:27:57,774 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fe18a1a - End of configuration.
[testng] [2024-09-17 01:27:57,838] [pool-1-thread-12] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile-1.lsm:
[testng] 01:27:57,838 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:27:57,838 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:57,839 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-17_01-27-57.log]
[testng] 01:27:57,840 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54469fd3 - End of configuration.
[testng] [2024-09-17 01:27:57,944] [pool-1-thread-11] Initializing /data/iplab/Color Image.IPL:
[testng] 01:27:57,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:27:57,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:57,945 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-17_01-27-57.log]
[testng] 01:27:57,946 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5afad74f - End of configuration.
[testng] [2024-09-17 01:27:57,954] [pool-1-thread-10] Initializing /data/iplab/10x Blood and Bacteria.IPL:
[testng] 01:27:57,954 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:27:57,954 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:57,955 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-17_01-27-57.log]
[testng] 01:27:57,955 |-INFO in ch.qos.logback.core.sift.SiftProcessor@bfb3c0 - End of configuration.
[testng] [2024-09-17 01:27:57,969] [pool-1-thread-9] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/Test2.dm3:
[testng] 01:27:57,969 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:27:57,969 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:57,970 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-17_01-27-57.log]
[testng] 01:27:57,971 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1da4d690 - End of configuration.
[testng] [2024-09-17 01:27:57,988] [pool-1-thread-8] Initializing /data/iplab/Actin.IPL:
[testng] 01:27:57,988 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:27:57,988 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:57,989 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-17_01-27-57.log]
[testng] 01:27:57,989 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7996bb6b - End of configuration.
[testng] [2024-09-17 01:27:57,998] [pool-1-thread-7] Initializing /data/iplab/Chromosomes.IPL:
[testng] 01:27:57,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:27:57,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:57,999 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-17_01-27-57.log]
[testng] 01:27:57,999 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36624c87 - End of configuration.
[testng] [2024-09-17 01:27:58,008] [pool-1-thread-6] Initializing /data/fluoview/Sample_TwoCH.TIF:
[testng] 01:27:58,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:27:58,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:58,009 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-17_01-27-58.log]
[testng] 01:27:58,009 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56380adc - End of configuration.
[testng] [2024-09-17 01:27:58,057] [pool-1-thread-5] Initializing /data/fluoview/sample_labled_XYZCh.tif:
[testng] 01:27:58,057 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:27:58,057 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:58,058 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-17_01-27-58.log]
[testng] 01:27:58,058 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ba6191a - End of configuration.
[testng] [2024-09-17 01:27:58,098] [pool-1-thread-4] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile-2.lsm:
[testng] 01:27:58,098 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:27:58,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:58,099 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-17_01-27-58.log]
[testng] 01:27:58,100 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75b09476 - End of configuration.
[testng] [2024-09-17 01:27:58,197] [pool-1-thread-3] Initializing /data/iplab/Color Histology.IPL:
[testng] 01:27:58,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:27:58,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:58,198 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-17_01-27-58.log]
[testng] 01:27:58,198 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48ef9df7 - End of configuration.
[testng] [2024-09-17 01:27:58,211] [pool-1-thread-2] Initializing /data/fluoview/Sample_XYZ.TIF:
[testng] 01:27:58,211 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:27:58,211 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:58,211 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-17_01-27-58.log]
[testng] 01:27:58,212 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64facc0f - End of configuration.
[testng] [2024-09-17 01:28:00,220] [pool-1-thread-8] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile--MultiTrack-1.lsm:
[testng] [2024-09-17 01:28:00,305] [pool-1-thread-3] Initializing /data/fluoview/Sample_XT.tif:
[testng] [2024-09-17 01:28:00,368] [pool-1-thread-11] Initializing /data/fluoview/Sample_XYT.TIF:
[testng] [2024-09-17 01:28:00,426] [pool-1-thread-7] Initializing /data/fluoview/SpineAnimation.tif:
[testng] [2024-09-17 01:28:00,484] [pool-1-thread-9] Initializing /data/iplab/Blend_Tritc.IPL:
[testng] [2024-09-17 01:28:00,503] [pool-1-thread-5] Initializing /data/fluoview/sample_labled_XYZTCh.tif:
[testng] [2024-09-17 01:28:00,550] [pool-1-thread-10] Initializing /data/iplab/Blend_DIC.IPL:
[testng] [2024-09-17 01:28:00,567] [pool-1-thread-2] Initializing /data/fluoview/SpineAnimation.avi:
[testng] [2024-09-17 01:28:00,589] [pool-1-thread-1] Initializing /data/iplab/16Bit XRay.IPL:
[testng] [2024-09-17 01:28:00,600] [pool-1-thread-6] Initializing /data/iplab/Blend_Final.IPL:
[testng] [2024-09-17 01:28:00,982] [pool-1-thread-1] Initializing /data/fluoview/sample_labled_XYTCh.tif:
[testng] [2024-09-17 01:28:01,258] [pool-1-thread-6] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/Test.dm3:
[testng] [2024-09-17 01:28:01,273] [pool-1-thread-10] Initializing /data/iplab/Blend_Fitc.IPL:
[testng] [2024-09-17 01:28:01,565] [pool-1-thread-9] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/test3.dm3:
[testng] [2024-09-17 01:28:01,579] [pool-1-thread-4] Initializing /data/iplab/3t3 Cell.IPL:
[testng] [2024-09-17 01:28:01,587] [pool-1-thread-5] Initializing /data/iplab/Blend_Dapi.IPL:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1484, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 40 seconds
Finished: SUCCESS