Skip to content
[Jenkins]Jenkins
log in

Console Output

Started by upstream project "BIOFORMATS-test-repo" build number 244
originally caused by:
 Started by upstream project "Trigger" build number 268
 originally caused by:
  Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7
[BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins11588254088753629137.sh
+ '[' cellomics = slidebook ']'
++ date +%u
+ '[' 7 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_38436_merge_ci -v /uod/idr/repos/curated/cellomics:/data -v /uod/idr-scratch/merge-ci/curated/cellomics:/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] 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] 02:33:25,509 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
   [testng] 02:33:25,511 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service.
   [testng] 02:33:25,511 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 02:33:25,512 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 02:33:25,512 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
   [testng] 02:33:25,512 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
   [testng] 02:33:25,513 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
   [testng] 02:33:25,513 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 02:33:25,513 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 02:33:25,514 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
   [testng] 02:33:25,514 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
   [testng] 02:33:25,514 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
   [testng] 02:33:25,683 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
   [testng] 02:33:25,684 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
   [testng] 02:33:25,707 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
   [testng] 02:33:25,708 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
   [testng] 02:33:25,713 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
   [testng] 02:33:25,714 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
   [testng] 02:33:25,714 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
   [testng] 02:33:25,714 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
   [testng] 02:33:25,714 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration.
   [testng] 02:33:25,715 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point
   [testng] 02:33:25,715 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 202 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
   [testng] [2024-11-03 02:33:25,725] [main] java.version = 17.0.2
   [testng] 02:33:25,729 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
   [testng] 02:33:25,729 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:33:25,771 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-03_02-33-25.log]
   [testng] 02:33:25,773 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration.
   [testng] [2024-11-03 02:33:25,775] [main] testng.directory = /data
   [testng] [2024-11-03 02:33:25,775] [main] testng.configDirectory = /config
   [testng] [2024-11-03 02:33:25,784] [main] testng.multiplier = 1.0
   [testng] [2024-11-03 02:33:25,784] [main] testng.in-memory = false
   [testng] [2024-11-03 02:33:25,785] [main] testng.allow-missing = false
   [testng] [2024-11-03 02:33:25,785] [main] user.language = en
   [testng] [2024-11-03 02:33:25,785] [main] user.country = ${user.country}
   [testng] [2024-11-03 02:33:25,785] [main] Maximum heap size = 15360 MB
   [testng] Scanning for files...
   [testng] [2024-11-03 02:33:41,915] [main] ----------------------------------------
   [testng] [2024-11-03 02:33:41,916] [main] Total files: 2539
   [testng] [2024-11-03 02:33:41,916] [main] Scan time: 16.13 s (6 ms/file)
   [testng] [2024-11-03 02:33:41,916] [main] ----------------------------------------
   [testng] Building list of tests...
   [testng] Ready to test 17 files
   [testng] [TestNG] Running:
   [testng]   Bio-Formats software test suite
   [testng] 
   [testng] [2024-11-03 02:33:49,886] [pool-1-thread-1] Initializing /data/samples/sparse-plate/plate_E03f00d0.C01: 
   [testng] 02:33:49,887 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
   [testng] 02:33:49,887 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:33:49,888 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-03_02-33-49.log]
   [testng] 02:33:49,889 |-INFO in ch.qos.logback.core.sift.SiftProcessor@210e88ce - End of configuration.
   [testng] [2024-11-03 02:33:50,019] [pool-1-thread-12] Initializing /data/samples/plate-size/plate_B03f00d0.C01: 
   [testng] 02:33:50,019 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
   [testng] 02:33:50,019 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:33:50,020 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-03_02-33-50.log]
   [testng] 02:33:50,020 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10afdf7 - End of configuration.
   [testng] [2024-11-03 02:33:50,134] [pool-1-thread-11] Initializing /data/omar/FB03f03o2.DIB: 
   [testng] 02:33:50,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
   [testng] 02:33:50,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:33:50,136 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-03_02-33-50.log]
   [testng] 02:33:50,136 |-INFO in ch.qos.logback.core.sift.SiftProcessor@581dc0fc - End of configuration.
   [testng] [2024-11-03 02:33:50,251] [pool-1-thread-10] Initializing /data/omar/FB03f00o2.C01: 
   [testng] 02:33:50,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
   [testng] 02:33:50,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:33:50,252 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-03_02-33-50.log]
   [testng] 02:33:50,252 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bac40d4 - End of configuration.
   [testng] [2024-11-03 02:33:50,371] [pool-1-thread-9] Initializing /data/qa-7352/test/MFGTMP-PC_130509120002_B02f00o1.C01: 
   [testng] 02:33:50,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
   [testng] 02:33:50,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:33:50,372 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-03_02-33-50.log]
   [testng] 02:33:50,372 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52e94a03 - End of configuration.
   [testng] [2024-11-03 02:33:50,543] [pool-1-thread-8] Initializing /data/harri/MFGTMP-PC_111018140003/MFGTMP-PC_111018140003_E04f00d0.C01: 
   [testng] 02:33:50,543 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
   [testng] 02:33:50,543 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:33:50,544 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-03_02-33-50.log]
   [testng] 02:33:50,544 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46b9a8cf - End of configuration.
   [testng] [2024-11-03 02:33:50,715] [pool-1-thread-7] Initializing /data/lee/AS_09125_050116030001_D03f00d0.DIB: 
   [testng] 02:33:50,715 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
   [testng] 02:33:50,715 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:33:50,716 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-03_02-33-50.log]
   [testng] 02:33:50,716 |-INFO in ch.qos.logback.core.sift.SiftProcessor@137e67f8 - End of configuration.
   [testng] [2024-11-03 02:33:50,817] [pool-1-thread-6] Initializing /data/qa-21720/AS_09125_050117190001_A14f00d0.DIB: 
   [testng] 02:33:50,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
   [testng] 02:33:50,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:33:50,818 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-03_02-33-50.log]
   [testng] 02:33:50,819 |-INFO in ch.qos.logback.core.sift.SiftProcessor@489f13d6 - End of configuration.
   [testng] [2024-11-03 02:33:50,920] [pool-1-thread-5] Initializing /data/public/BBBC001/AS_09125_050118150001_A03f00d0.DIB: 
   [testng] 02:33:50,920 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
   [testng] 02:33:50,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:33:50,921 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-03_02-33-50.log]
   [testng] 02:33:50,922 |-INFO in ch.qos.logback.core.sift.SiftProcessor@525738bb - End of configuration.
   [testng] [2024-11-03 02:33:51,022] [pool-1-thread-4] Initializing /data/johannes/MFGTMP_081222130005_E07f00d0.C01: 
   [testng] 02:33:51,023 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
   [testng] 02:33:51,023 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:33:51,024 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-03_02-33-51.log]
   [testng] 02:33:51,024 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f8f4faa - End of configuration.
   [testng] [2024-11-03 02:33:51,139] [pool-1-thread-3] Initializing /data/lee/icd002235_090127090001_a01f00d1.c01: 
   [testng] 02:33:51,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
   [testng] 02:33:51,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:33:51,140 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-03_02-33-51.log]
   [testng] 02:33:51,140 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27d529e0 - End of configuration.
   [testng] [2024-11-03 02:33:51,256] [pool-1-thread-2] Initializing /data/omar/FB03f00d0.C01: 
   [testng] 02:33:51,256 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
   [testng] 02:33:51,256 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:33:51,257 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-03_02-33-51.log]
   [testng] 02:33:51,257 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c3b9b85 - End of configuration.
   [testng] [2024-11-03 02:33:53,666] [pool-1-thread-7] Initializing /data/qa-7352/test/MFGTMP-PC_130509120002_B02f00d0.C01: 
   [testng] [2024-11-03 02:33:53,952] [pool-1-thread-11] Initializing /data/samples/different-field-count/plate_B03f00d0.C01: 
   [testng] [2024-11-03 02:33:54,499] [pool-1-thread-4] Initializing /data/johannes/MFGTMP_081128200001_A02f239d1.C01: 
   [testng] [2024-11-03 02:33:54,694] [pool-1-thread-3] Initializing /data/omar/FB03f00d1.C01: 
   [testng] [2024-11-03 02:33:54,890] [pool-1-thread-10] Initializing /data/omar/FB03f00o1.C01: 
   [testng] 
   [testng] ===============================================
   [testng] Bio-Formats software test suite
   [testng] Total tests run: 901, Failures: 0, Skips: 0
   [testng] ===============================================
   [testng] 

BUILD SUCCESSFUL
Total time: 15 minutes 10 seconds
Finished: SUCCESS