Skip to content
[Jenkins]Jenkins
log in

Console Output

Started by upstream project "BIOFORMATS-test-repo" build number 4
originally caused by:
 Started by upstream project "Trigger" build number 5
 originally caused by:
  Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2
[BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins3191956408704429244.sh
+ '[' imaris = slidebook ']'
++ date +%u
+ '[' 7 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_579_merge_ci -v /uod/idr/repos/curated/imaris:/data -v /uod/idr-scratch/merge-ci/curated/imaris:/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] 01:39:12,281 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
   [testng] 01:39:12,282 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service.
   [testng] 01:39:12,282 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 01:39:12,283 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 01:39:12,284 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
   [testng] 01:39:12,284 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
   [testng] 01:39:12,285 |-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] 01:39:12,285 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 01:39:12,285 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 01:39:12,286 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
   [testng] 01:39:12,286 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
   [testng] 01:39:12,286 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
   [testng] 01:39:12,477 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
   [testng] 01:39:12,477 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
   [testng] 01:39:12,509 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
   [testng] 01:39:12,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
   [testng] 01:39:12,518 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
   [testng] 01:39:12,518 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
   [testng] 01:39:12,518 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
   [testng] 01:39:12,519 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
   [testng] 01:39:12,519 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration.
   [testng] 01:39:12,521 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point
   [testng] 01:39:12,521 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 236 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
   [testng] [2024-03-17 01:39:12,533] [main] java.version = 17.0.2
   [testng] 01:39:12,537 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
   [testng] 01:39:12,537 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:39:12,586 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-17_01-39-12.log]
   [testng] 01:39:12,588 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration.
   [testng] [2024-03-17 01:39:12,591] [main] testng.directory = /data
   [testng] [2024-03-17 01:39:12,592] [main] testng.configDirectory = /config
   [testng] [2024-03-17 01:39:12,607] [main] testng.multiplier = 1.0
   [testng] [2024-03-17 01:39:12,609] [main] testng.in-memory = false
   [testng] [2024-03-17 01:39:12,609] [main] testng.allow-missing = false
   [testng] [2024-03-17 01:39:12,609] [main] user.language = en
   [testng] [2024-03-17 01:39:12,609] [main] user.country = ${user.country}
   [testng] [2024-03-17 01:39:12,610] [main] Maximum heap size = 15360 MB
   [testng] Scanning for files...
   [testng] [2024-03-17 01:39:29,227] [main] ----------------------------------------
   [testng] [2024-03-17 01:39:29,227] [main] Total files: 67
   [testng] [2024-03-17 01:39:29,227] [main] Scan time: 16.616 s (248 ms/file)
   [testng] [2024-03-17 01:39:29,227] [main] ----------------------------------------
   [testng] Building list of tests...
   [testng] Ready to test 59 files
   [testng] [TestNG] Running:
   [testng]   Bio-Formats software test suite
   [testng] 
   [testng] [2024-03-17 01:39:56,799] [pool-1-thread-1] Initializing /data/generated/mri-stack-original.ims: 
   [testng] 01:39:56,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
   [testng] 01:39:56,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:39:56,802 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-17_01-39-56.log]
   [testng] 01:39:56,803 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2defdcf - End of configuration.
   [testng] [2024-03-17 01:39:56,915] [pool-1-thread-12] Initializing /data/jason/imaris_5_5_demoimages/HeLaCell.ims: 
   [testng] 01:39:56,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
   [testng] 01:39:56,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:39:56,916 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-17_01-39-56.log]
   [testng] 01:39:56,916 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3647133b - End of configuration.
   [testng] [2024-03-17 01:39:57,173] [pool-1-thread-11] Initializing /data/public/davemason/TransFactors_2C_SRRF_IMS3.ims: 
   [testng] 01:39:57,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
   [testng] 01:39:57,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:39:57,174 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-17_01-39-57.log]
   [testng] 01:39:57,174 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a7935a1 - End of configuration.
   [testng] [2024-03-17 01:39:57,451] [pool-1-thread-10] Initializing /data/public/davemason/Convallaria_3C_1T_2x2grid_confocal.ims: 
   [testng] 01:39:57,452 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
   [testng] 01:39:57,452 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:39:57,453 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-17_01-39-57.log]
   [testng] 01:39:57,453 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22fed631 - End of configuration.
   [testng] [2024-03-17 01:39:57,732] [pool-1-thread-9] Initializing /data/jason/imaris_5_5_demoimages/R18Demo.ims: 
   [testng] 01:39:57,732 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
   [testng] 01:39:57,732 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:39:57,733 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-17_01-39-57.log]
   [testng] 01:39:57,733 |-INFO in ch.qos.logback.core.sift.SiftProcessor@153ca8a0 - End of configuration.
   [testng] [2024-03-17 01:39:58,009] [pool-1-thread-8] Initializing /data/public/davemason/TransFactors_2C_SRRF.ims: 
   [testng] 01:39:58,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
   [testng] 01:39:58,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:39:58,010 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-17_01-39-58.log]
   [testng] 01:39:58,011 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60804ce6 - End of configuration.
   [testng] [2024-03-17 01:39:58,281] [pool-1-thread-7] Initializing /data/generated/10-31_E_t0013.ims: 
   [testng] 01:39:58,281 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
   [testng] 01:39:58,281 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:39:58,282 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-17_01-39-58.log]
   [testng] 01:39:58,283 |-INFO in ch.qos.logback.core.sift.SiftProcessor@16c40cec - End of configuration.
   [testng] [2024-03-17 01:39:58,398] [pool-1-thread-6] Initializing /data/generated/10-31_E_t0000.ims: 
   [testng] 01:39:58,398 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
   [testng] 01:39:58,398 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:39:58,399 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-17_01-39-58.log]
   [testng] 01:39:58,399 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63db178a - End of configuration.
   [testng] [2024-03-17 01:39:58,513] [pool-1-thread-5] Initializing /data/public/davemason/Convallaria_3C_1T_2x2grid_confocal_IMS3.ims: 
   [testng] 01:39:58,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
   [testng] 01:39:58,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:39:58,514 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-17_01-39-58.log]
   [testng] 01:39:58,514 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52d900e3 - End of configuration.
   [testng] [2024-03-17 01:39:58,820] [pool-1-thread-4] Initializing /data/kay/Imaris503_test_Kay.ims: 
   [testng] 01:39:58,821 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
   [testng] 01:39:58,821 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:39:58,822 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-17_01-39-58.log]
   [testng] 01:39:58,822 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20c43d65 - End of configuration.
   [testng] [2024-03-17 01:39:59,113] [pool-1-thread-3] Initializing /data/generated/10-31_E_t0009.ims: 
   [testng] 01:39:59,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
   [testng] 01:39:59,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:39:59,115 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-17_01-39-59.log]
   [testng] 01:39:59,115 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1643f997 - End of configuration.
   [testng] [2024-03-17 01:39:59,246] [pool-1-thread-2] Initializing /data/generated/10-31_E_t0007.ims: 
   [testng] 01:39:59,246 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
   [testng] 01:39:59,246 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:39:59,247 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-17_01-39-59.log]
   [testng] 01:39:59,248 |-INFO in ch.qos.logback.core.sift.SiftProcessor@454f1806 - End of configuration.

BUILD SUCCESSFUL
Total time: 3 minutes 39 seconds
Finished: SUCCESS