Skip to content
[Jenkins]Jenkins
log in

Console Output

Started by upstream project "BIOFORMATS-test-repo" build number 364
originally caused by:
 Started by upstream project "Trigger" build number 390
 originally caused by:
  Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder
[BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins10709155536266782972.sh
+ '[' leica-tcs = slidebook ']'
++ date +%u
+ '[' 2 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_58106_merge_ci -v /uod/idr/repos/curated/leica-tcs:/data -v /uod/idr-scratch/merge-ci/curated/leica-tcs:/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] 03:58:49,591 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15
   [testng] 03:58:49,593 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - No custom configurators were discovered as a service.
   [testng] 03:58:49,593 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 03:58:49,594 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 03:58:49,595 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
   [testng] 03:58:49,596 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
   [testng] 03:58:49,596 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
   [testng] 03:58:49,596 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 03:58:49,597 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 03:58:49,597 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
   [testng] 03:58:49,598 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
   [testng] 03:58:49,598 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
   [testng] 03:58:49,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
   [testng] 03:58:49,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
   [testng] 03:58:49,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
   [testng] 03:58:49,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
   [testng] 03:58:49,805 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
   [testng] 03:58:49,806 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
   [testng] 03:58:49,806 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
   [testng] 03:58:49,806 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
   [testng] 03:58:49,806 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@65c7a252 - End of configuration.
   [testng] 03:58:49,807 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@38cee291 - Registering current configuration as safe fallback point
   [testng] 03:58:49,807 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 210 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
   [testng] [2025-03-04 03:58:49,816] [main] java.version = 11.0.16
   [testng] 03:58:49,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
   [testng] 03:58:49,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 03:58:49,864 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-04_03-58-49.log]
   [testng] 03:58:49,866 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13d73f29 - End of configuration.
   [testng] [2025-03-04 03:58:49,868] [main] testng.directory = /data
   [testng] [2025-03-04 03:58:49,868] [main] testng.configDirectory = /config
   [testng] [2025-03-04 03:58:49,878] [main] testng.multiplier = 1.0
   [testng] [2025-03-04 03:58:49,879] [main] testng.in-memory = false
   [testng] [2025-03-04 03:58:49,879] [main] testng.allow-missing = false
   [testng] [2025-03-04 03:58:49,879] [main] user.language = en
   [testng] [2025-03-04 03:58:49,879] [main] user.country = ${user.country}
   [testng] [2025-03-04 03:58:49,879] [main] Maximum heap size = 15360 MB
   [testng] Scanning for files...
   [testng] [2025-03-04 03:59:02,866] [main] ----------------------------------------
   [testng] [2025-03-04 03:59:02,866] [main] Total files: 944
   [testng] [2025-03-04 03:59:02,867] [main] Scan time: 12.987 s (13 ms/file)
   [testng] [2025-03-04 03:59:02,867] [main] ----------------------------------------
   [testng] Building list of tests...
   [testng] Ready to test 15 files
   [testng] [TestNG] Running:
   [testng]   Bio-Formats software test suite
   [testng] 
   [testng] [2025-03-04 04:00:28,492] [pool-1-thread-1] Initializing /data/brian/Series002_z00_ch00.tif: 
   [testng] 04:00:28,493 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
   [testng] 04:00:28,493 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:00:28,494 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-04_04-00-28.log]
   [testng] 04:00:28,495 |-INFO in ch.qos.logback.core.sift.SiftProcessor@208aea16 - End of configuration.
   [testng] [2025-03-04 04:00:29,824] [pool-1-thread-12] Initializing /data/dave/series 35/042911_Series035_t00_z000_ch00.tif: 
   [testng] 04:00:29,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
   [testng] 04:00:29,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:00:29,825 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-04_04-00-29.log]
   [testng] 04:00:29,825 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12d7eaf6 - End of configuration.
   [testng] [2025-03-04 04:01:17,089] [pool-1-thread-11] Initializing /data/stjude/AntoDay4dblcatdataGRP.tif: 
   [testng] 04:01:17,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
   [testng] 04:01:17,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:01:17,090 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-04_04-01-17.log]
   [testng] 04:01:17,091 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30ef02f - End of configuration.
   [testng] [2025-03-04 04:01:18,311] [pool-1-thread-10] Initializing /data/stjude/AntoDay4dblmyGRP.tif: 
   [testng] 04:01:18,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
   [testng] 04:01:18,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:01:18,312 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-04_04-01-18.log]
   [testng] 04:01:18,312 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69a28ded - End of configuration.
   [testng] [2025-03-04 04:01:19,384] [pool-1-thread-9] Initializing /data/stjude/AntoDayzerocy3OVP.tif: 
   [testng] 04:01:19,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
   [testng] 04:01:19,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:01:19,385 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-04_04-01-19.log]
   [testng] 04:01:19,385 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c158194 - End of configuration.
   [testng] [2025-03-04 04:01:20,589] [pool-1-thread-8] Initializing /data/brian/Series002_z01.tif: 
   [testng] 04:01:20,589 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
   [testng] 04:01:20,589 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:01:20,590 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-04_04-01-20.log]
   [testng] 04:01:20,590 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b730b47 - End of configuration.
   [testng] [2025-03-04 04:01:22,189] [pool-1-thread-7] Initializing /data/stjude/Antoday1dblmysglGRP.tif: 
   [testng] 04:01:22,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
   [testng] 04:01:22,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:01:22,191 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-04_04-01-22.log]
   [testng] 04:01:22,191 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37c683f3 - End of configuration.
   [testng] [2025-03-04 04:01:23,266] [pool-1-thread-6] Initializing /data/stjude/AntoDay1dblGRP.tif: 
   [testng] 04:01:23,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
   [testng] 04:01:23,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:01:23,267 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-04_04-01-23.log]
   [testng] 04:01:23,268 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37fa8409 - End of configuration.
   [testng] [2025-03-04 04:01:24,435] [pool-1-thread-5] Initializing /data/stjude/AntoDayzerocy3GRP.tif: 
   [testng] 04:01:24,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
   [testng] 04:01:24,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:01:24,436 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-04_04-01-24.log]
   [testng] 04:01:24,436 |-INFO in ch.qos.logback.core.sift.SiftProcessor@de27ca - End of configuration.
   [testng] [2025-03-04 04:01:25,715] [pool-1-thread-4] Initializing /data/martin/Series028_z00_ch00.tif: 
   [testng] 04:01:25,715 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
   [testng] 04:01:25,715 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:01:25,715 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-04_04-01-25.log]
   [testng] 04:01:25,716 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32602ca7 - End of configuration.
   [testng] [2025-03-04 04:01:27,404] [pool-1-thread-3] Initializing /data/stjude/AntoDay1cy3/c01f0001.TIF: 
   [testng] 04:01:27,404 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
   [testng] 04:01:27,404 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:01:27,404 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-04_04-01-27.log]
   [testng] 04:01:27,405 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3dd6691a - End of configuration.
   [testng] [2025-03-04 04:01:28,450] [pool-1-thread-2] Initializing /data/stjude/AntoDay4dblmy2GRP.tif: 
   [testng] 04:01:28,450 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
   [testng] 04:01:28,450 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:01:28,450 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-04_04-01-28.log]
   [testng] 04:01:28,451 |-INFO in ch.qos.logback.core.sift.SiftProcessor@199d3c1e - End of configuration.
   [testng] [2025-03-04 04:01:37,271] [pool-1-thread-3] Initializing /data/stjude/Antoday1dblcat2dataGRP.tif: 
   [testng] [2025-03-04 04:01:40,966] [pool-1-thread-8] Initializing /data/primate/Leica_Image.tif: 
   [testng] [2025-03-04 04:01:42,317] [pool-1-thread-10] Initializing /data/stjude/Antoday1dblcatsglGRP.tif: 
   [testng] 05:22:28,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
   [testng] 05:22:28,688 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 05:22:28,689 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-04_05-22-28.log]
   [testng] 05:22:28,689 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d157493 - End of configuration.
   [testng] 
   [testng] ===============================================
   [testng] Bio-Formats software test suite
   [testng] Total tests run: 795, Failures: 0, Skips: 0
   [testng] ===============================================
   [testng] 

BUILD SUCCESSFUL
Total time: 83 minutes 44 seconds
Finished: SUCCESS