Skip to content
[Jenkins]Jenkins
log in

Console Output

Started by upstream project "BIOFORMATS-test-repo" build number 312
originally caused by:
 Started by upstream project "Trigger" build number 334
 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/jenkins13190681002568587737.sh
+ '[' minc = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_49450_merge_ci -v /uod/idr/repos/curated/minc:/data -v /uod/idr-scratch/merge-ci/curated/minc:/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] 01:42:28,869 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
   [testng] 01:42:28,871 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service.
   [testng] 01:42:28,871 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 01:42:28,872 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 01:42:28,872 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
   [testng] 01:42:28,873 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
   [testng] 01:42:28,873 |-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] 01:42:28,873 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 01:42:28,873 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 01:42:28,874 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
   [testng] 01:42:28,874 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
   [testng] 01:42:28,875 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
   [testng] 01:42:29,051 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
   [testng] 01:42:29,051 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
   [testng] 01:42:29,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
   [testng] 01:42:29,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
   [testng] 01:42:29,081 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
   [testng] 01:42:29,081 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
   [testng] 01:42:29,081 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
   [testng] 01:42:29,081 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
   [testng] 01:42:29,081 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration.
   [testng] 01:42:29,083 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point
   [testng] 01:42:29,083 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 210 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
   [testng] [2025-01-08 01:42:29,092] [main] java.version = 17.0.2
   [testng] 01:42:29,096 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
   [testng] 01:42:29,096 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:42:29,142 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-08_01-42-29.log]
   [testng] 01:42:29,143 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration.
   [testng] [2025-01-08 01:42:29,145] [main] testng.directory = /data
   [testng] [2025-01-08 01:42:29,146] [main] testng.configDirectory = /config
   [testng] [2025-01-08 01:42:29,154] [main] testng.multiplier = 1.0
   [testng] [2025-01-08 01:42:29,155] [main] testng.in-memory = false
   [testng] [2025-01-08 01:42:29,155] [main] testng.allow-missing = false
   [testng] [2025-01-08 01:42:29,156] [main] user.language = en
   [testng] [2025-01-08 01:42:29,156] [main] user.country = ${user.country}
   [testng] [2025-01-08 01:42:29,156] [main] Maximum heap size = 15360 MB
   [testng] Scanning for files...
   [testng] [2025-01-08 01:42:29,729] [main] ----------------------------------------
   [testng] [2025-01-08 01:42:29,729] [main] Total files: 15
   [testng] [2025-01-08 01:42:29,729] [main] Scan time: 0.573 s (38 ms/file)
   [testng] [2025-01-08 01:42:29,729] [main] ----------------------------------------
   [testng] Building list of tests...
   [testng] Ready to test 15 files
   [testng] [TestNG] Running:
   [testng]   Bio-Formats software test suite
   [testng] 
   [testng] [2025-01-08 01:42:42,912] [pool-1-thread-1] Initializing /data/samples/ICBM/icbm_template_2.00mm.mnc: 
   [testng] 01:42:42,912 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
   [testng] 01:42:42,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:42:42,914 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-08_01-42-42.log]
   [testng] 01:42:42,914 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1171dc57 - End of configuration.
   [testng] [2025-01-08 01:42:43,286] [pool-1-thread-12] Initializing /data/bigbrain/pm6479o.mnc: 
   [testng] 01:42:43,287 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
   [testng] 01:42:43,287 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:42:43,288 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-08_01-42-43.log]
   [testng] 01:42:43,288 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79e01ce7 - End of configuration.
   [testng] [2025-01-08 01:42:44,515] [pool-1-thread-11] Initializing /data/qa-17215/IBSR01.mnc: 
   [testng] 01:42:44,516 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
   [testng] 01:42:44,516 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:42:44,517 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-08_01-42-44.log]
   [testng] 01:42:44,517 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a3cbf7a - End of configuration.
   [testng] [2025-01-08 01:42:44,935] [pool-1-thread-10] Initializing /data/samples/ICBM/icbm_template_6.00mm.mnc: 
   [testng] 01:42:44,936 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
   [testng] 01:42:44,936 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:42:44,937 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-08_01-42-44.log]
   [testng] 01:42:44,937 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a2b5e54 - End of configuration.
   [testng] [2025-01-08 01:42:45,287] [pool-1-thread-9] Initializing /data/bigbrain/full16_400um_2009b_sym.mnc: 
   [testng] 01:42:45,287 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
   [testng] 01:42:45,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:42:45,288 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-08_01-42-45.log]
   [testng] 01:42:45,289 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f1ffcbd - End of configuration.
   [testng] [2025-01-08 01:42:47,903] [pool-1-thread-8] Initializing /data/samples/ICBM/icbm_template_zero.75mm.mnc: 
   [testng] 01:42:47,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
   [testng] 01:42:47,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:42:47,905 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-08_01-42-47.log]
   [testng] 01:42:47,906 |-INFO in ch.qos.logback.core.sift.SiftProcessor@765b0bf3 - End of configuration.
   [testng] [2025-01-08 01:42:48,303] [pool-1-thread-7] Initializing /data/samples/ICBM/icbm_template_one.50mm.mnc: 
   [testng] 01:42:48,303 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
   [testng] 01:42:48,303 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:42:48,304 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-08_01-42-48.log]
   [testng] 01:42:48,304 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33710184 - End of configuration.
   [testng] [2025-01-08 01:42:49,083] [pool-1-thread-6] Initializing /data/samples/ICBM/icbm_template_zero.50mm.mnc: 
   [testng] 01:42:49,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
   [testng] 01:42:49,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:42:49,084 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-08_01-42-49.log]
   [testng] 01:42:49,084 |-INFO in ch.qos.logback.core.sift.SiftProcessor@655cdfb9 - End of configuration.
   [testng] [2025-01-08 01:42:49,532] [pool-1-thread-5] Initializing /data/samples/ICBM/icbm_template_one.00mm.mnc: 
   [testng] 01:42:49,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
   [testng] 01:42:49,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:42:49,534 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-08_01-42-49.log]
   [testng] 01:42:49,534 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f54e65a - End of configuration.
   [testng] [2025-01-08 01:42:49,885] [pool-1-thread-4] Initializing /data/samples/ICBM/icbm_atlas_cerebellum_avg_53_mask_1mm.mnc: 
   [testng] 01:42:49,885 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
   [testng] 01:42:49,885 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:42:49,886 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-08_01-42-49.log]
   [testng] 01:42:49,886 |-INFO in ch.qos.logback.core.sift.SiftProcessor@663335ab - End of configuration.
   [testng] [2025-01-08 01:42:50,266] [pool-1-thread-3] Initializing /data/bigbrain/8-bit_full_400um_2009b_sym.mnc: 
   [testng] 01:42:50,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
   [testng] 01:42:50,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:42:50,267 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-08_01-42-50.log]
   [testng] 01:42:50,268 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44b35ac9 - End of configuration.
   [testng] [2025-01-08 01:42:51,953] [pool-1-thread-2] Initializing /data/samples/ICBM/icbm_template_4.00mm.mnc: 
   [testng] 01:42:51,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
   [testng] 01:42:51,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:42:51,954 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-08_01-42-51.log]
   [testng] 01:42:51,954 |-INFO in ch.qos.logback.core.sift.SiftProcessor@374cf566 - End of configuration.

BUILD SUCCESSFUL
Total time: 48 seconds
Finished: SUCCESS