Skip to content
[Jenkins]Jenkins
log in

Console Output

Started by upstream project "BIOFORMATS-test-repo" build number 127
originally caused by:
 Started by upstream project "Trigger" build number 144
 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/jenkins8223182490207632370.sh
+ '[' amira = slidebook ']'
++ date +%u
+ '[' 7 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_19841_merge_ci -v /uod/idr/repos/curated/amira:/data -v /uod/idr-scratch/merge-ci/curated/amira:/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] 01:22:24,994 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
   [testng] 01:22:24,995 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service.
   [testng] 01:22:24,995 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 01:22:24,996 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 01:22:24,997 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
   [testng] 01:22:24,997 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
   [testng] 01:22:24,998 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
   [testng] 01:22:24,998 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 01:22:24,998 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 01:22:24,999 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
   [testng] 01:22:24,999 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
   [testng] 01:22:24,999 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
   [testng] 01:22:25,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
   [testng] 01:22:25,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
   [testng] 01:22:25,198 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
   [testng] 01:22:25,198 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
   [testng] 01:22:25,203 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
   [testng] 01:22:25,203 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
   [testng] 01:22:25,203 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
   [testng] 01:22:25,204 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
   [testng] 01:22:25,204 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration.
   [testng] 01:22:25,205 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point
   [testng] 01:22:25,205 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 207 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
   [testng] [2024-07-21 01:22:25,214] [main] java.version = 17.0.2
   [testng] 01:22:25,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
   [testng] 01:22:25,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:22:25,266 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-21_01-22-25.log]
   [testng] 01:22:25,268 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration.
   [testng] [2024-07-21 01:22:25,270] [main] testng.directory = /data
   [testng] [2024-07-21 01:22:25,271] [main] testng.configDirectory = /config
   [testng] [2024-07-21 01:22:25,281] [main] testng.multiplier = 1.0
   [testng] [2024-07-21 01:22:25,282] [main] testng.in-memory = false
   [testng] [2024-07-21 01:22:25,282] [main] testng.allow-missing = false
   [testng] [2024-07-21 01:22:25,282] [main] user.language = en
   [testng] [2024-07-21 01:22:25,283] [main] user.country = ${user.country}
   [testng] [2024-07-21 01:22:25,283] [main] Maximum heap size = 15360 MB
   [testng] Scanning for files...
   [testng] [2024-07-21 01:22:25,887] [main] ----------------------------------------
   [testng] [2024-07-21 01:22:25,887] [main] Total files: 15
   [testng] [2024-07-21 01:22:25,887] [main] Scan time: 0.604 s (40 ms/file)
   [testng] [2024-07-21 01:22:25,888] [main] ----------------------------------------
   [testng] Building list of tests...
   [testng] Ready to test 12 files
   [testng] [TestNG] Running:
   [testng]   Bio-Formats software test suite
   [testng] 
   [testng] [2024-07-21 01:22:26,960] [pool-1-thread-1] Initializing /data/johannes/template.labels: 
   [testng] 01:22:26,960 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
   [testng] 01:22:26,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:22:26,962 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-21_01-22-26.log]
   [testng] 01:22:26,962 |-INFO in ch.qos.logback.core.sift.SiftProcessor@349bfc81 - End of configuration.
   [testng] [2024-07-21 01:22:26,987] [pool-1-thread-12] Initializing /data/jeremy/Virus_Membrane7.am: 
   [testng] 01:22:26,987 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
   [testng] 01:22:26,988 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:22:26,989 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-21_01-22-26.log]
   [testng] 01:22:26,990 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27cc0125 - End of configuration.
   [testng] [2024-07-21 01:22:27,041] [pool-1-thread-11] Initializing /data/public/ignacio/test.am: 
   [testng] 01:22:27,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
   [testng] 01:22:27,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:22:27,042 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-21_01-22-27.log]
   [testng] 01:22:27,043 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bfbb9e1 - End of configuration.
   [testng] [2024-07-21 01:22:27,057] [pool-1-thread-10] Initializing /data/public/imagesc-50585/BF_CheckAmira.am: 
   [testng] 01:22:27,057 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
   [testng] 01:22:27,057 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:22:27,058 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-21_01-22-27.log]
   [testng] 01:22:27,059 |-INFO in ch.qos.logback.core.sift.SiftProcessor@372b27c3 - End of configuration.
   [testng] [2024-07-21 01:22:27,076] [pool-1-thread-9] Initializing /data/jeremy/Hiv_spikes.am: 
   [testng] 01:22:27,076 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
   [testng] 01:22:27,076 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:22:27,077 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-21_01-22-27.log]
   [testng] 01:22:27,077 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74c530fd - End of configuration.
   [testng] [2024-07-21 01:22:27,105] [pool-1-thread-8] Initializing /data/samples/emptykey/test.am: 
   [testng] 01:22:27,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
   [testng] 01:22:27,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:22:27,106 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-21_01-22-27.log]
   [testng] 01:22:27,106 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2653f72b - End of configuration.
   [testng] [2024-07-21 01:22:27,120] [pool-1-thread-7] Initializing /data/jcb/201108088/Haberman-Fig4A-original.am: 
   [testng] 01:22:27,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
   [testng] 01:22:27,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:22:27,121 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-21_01-22-27.log]
   [testng] 01:22:27,122 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56f83690 - End of configuration.
   [testng] [2024-07-21 01:22:27,158] [pool-1-thread-6] Initializing /data/jeremy/Virus_Membrane7-screenshot.PNG: 
   [testng] 01:22:27,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
   [testng] 01:22:27,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:22:27,159 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-21_01-22-27.log]
   [testng] 01:22:27,160 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1cb74978 - End of configuration.
   [testng] [2024-07-21 01:22:27,172] [pool-1-thread-5] Initializing /data/public/imagesc-50585/BF_CheckMIB.am: 
   [testng] 01:22:27,172 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
   [testng] 01:22:27,172 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:22:27,173 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-21_01-22-27.log]
   [testng] 01:22:27,173 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d3c5000 - End of configuration.
   [testng] [2024-07-21 01:22:27,185] [pool-1-thread-4] Initializing /data/ilya/test.am: 
   [testng] 01:22:27,185 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
   [testng] 01:22:27,185 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:22:27,186 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-21_01-22-27.log]
   [testng] 01:22:27,186 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9c27da4 - End of configuration.
   [testng] [2024-07-21 01:22:27,230] [pool-1-thread-3] Initializing /data/public/imagesc-50585/BF_Check.tif: 
   [testng] 01:22:27,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
   [testng] 01:22:27,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:22:27,231 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-21_01-22-27.log]
   [testng] 01:22:27,232 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1dc24ef9 - End of configuration.
   [testng] [2024-07-21 01:22:27,263] [pool-1-thread-2] Initializing /data/johannes/template.grey: 
   [testng] 01:22:27,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
   [testng] 01:22:27,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:22:27,264 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-21_01-22-27.log]
   [testng] 01:22:27,265 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d654a70 - End of configuration.
   [testng] 
   [testng] ===============================================
   [testng] Bio-Formats software test suite
   [testng] Total tests run: 636, Failures: 0, Skips: 0
   [testng] ===============================================
   [testng] 

BUILD SUCCESSFUL
Total time: 11 seconds
Finished: SUCCESS