Skip to content
[Jenkins]Jenkins
log in

Console Output

Started by upstream project "BIOFORMATS-test-repo" build number 67
originally caused by:
 Started by upstream project "Trigger" build number 75
 originally caused by:
  Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3
[BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins4617735488379735052.sh
+ '[' mrc = slidebook ']'
++ date +%u
+ '[' 6 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_10037_merge_ci -v /uod/idr/repos/curated/mrc:/data -v /uod/idr-scratch/merge-ci/curated/mrc:/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] 01:37:37,553 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
   [testng] 01:37:37,554 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service.
   [testng] 01:37:37,554 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 01:37:37,555 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 01:37:37,556 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
   [testng] 01:37:37,556 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
   [testng] 01:37:37,556 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
   [testng] 01:37:37,556 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 01:37:37,557 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 01:37:37,557 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
   [testng] 01:37:37,558 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
   [testng] 01:37:37,558 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
   [testng] 01:37:37,737 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
   [testng] 01:37:37,737 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
   [testng] 01:37:37,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
   [testng] 01:37:37,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
   [testng] 01:37:37,779 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
   [testng] 01:37:37,779 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
   [testng] 01:37:37,779 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
   [testng] 01:37:37,780 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
   [testng] 01:37:37,780 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration.
   [testng] 01:37:37,781 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point
   [testng] 01:37:37,781 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 224 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
   [testng] [2024-05-18 01:37:37,795] [main] java.version = 11.0.16
   [testng] 01:37:37,799 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
   [testng] 01:37:37,799 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:37:37,854 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-18_01-37-37.log]
   [testng] 01:37:37,857 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
   [testng] [2024-05-18 01:37:37,859] [main] testng.directory = /data
   [testng] [2024-05-18 01:37:37,860] [main] testng.configDirectory = /config
   [testng] [2024-05-18 01:37:37,870] [main] testng.multiplier = 1.0
   [testng] [2024-05-18 01:37:37,871] [main] testng.in-memory = false
   [testng] [2024-05-18 01:37:37,871] [main] testng.allow-missing = false
   [testng] [2024-05-18 01:37:37,871] [main] user.language = en
   [testng] [2024-05-18 01:37:37,871] [main] user.country = ${user.country}
   [testng] [2024-05-18 01:37:37,871] [main] Maximum heap size = 15360 MB
   [testng] Scanning for files...
   [testng] [2024-05-18 01:37:39,122] [main] ----------------------------------------
   [testng] [2024-05-18 01:37:39,122] [main] Total files: 20
   [testng] [2024-05-18 01:37:39,122] [main] Scan time: 1.25 s (62 ms/file)
   [testng] [2024-05-18 01:37:39,122] [main] ----------------------------------------
   [testng] Building list of tests...
   [testng] Ready to test 20 files
   [testng] [TestNG] Running:
   [testng]   Bio-Formats software test suite
   [testng] 
   [testng] [2024-05-18 01:37:39,616] [pool-1-thread-1] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: 
   [testng] 01:37:39,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
   [testng] 01:37:39,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:37:39,619 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-18_01-37-39.log]
   [testng] 01:37:39,620 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5198198 - End of configuration.
   [testng] [2024-05-18 01:37:39,639] [pool-1-thread-12] Initializing /data/ascb/c191.st: 
   [testng] 01:37:39,640 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
   [testng] 01:37:39,640 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:37:39,641 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-18_01-37-39.log]
   [testng] 01:37:39,642 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b859d5b - End of configuration.
   [testng] [2024-05-18 01:37:39,656] [pool-1-thread-11] Initializing /data/dan/two.mrc: 
   [testng] 01:37:39,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
   [testng] 01:37:39,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:37:39,657 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-18_01-37-39.log]
   [testng] 01:37:39,657 |-INFO in ch.qos.logback.core.sift.SiftProcessor@999d128 - End of configuration.
   [testng] [2024-05-18 01:37:39,675] [pool-1-thread-10] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc: 
   [testng] 01:37:39,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
   [testng] 01:37:39,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:37:39,676 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-18_01-37-39.log]
   [testng] 01:37:39,676 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42bcb890 - End of configuration.
   [testng] [2024-05-18 01:37:39,712] [pool-1-thread-9] Initializing /data/samples/golgi.mrc: 
   [testng] 01:37:39,712 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
   [testng] 01:37:39,713 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:37:39,713 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-18_01-37-39.log]
   [testng] 01:37:39,714 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b77fe1a - End of configuration.
   [testng] [2024-05-18 01:37:39,794] [pool-1-thread-8] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: 
   [testng] 01:37:39,794 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
   [testng] 01:37:39,794 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:37:39,795 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-18_01-37-39.log]
   [testng] 01:37:39,795 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f395a0a - End of configuration.
   [testng] [2024-05-18 01:37:39,814] [pool-1-thread-7] Initializing /data/bioformats2raw-198/test_uint8.mrc: 
   [testng] 01:37:39,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
   [testng] 01:37:39,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:37:39,815 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-18_01-37-39.log]
   [testng] 01:37:39,815 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a182810 - End of configuration.
   [testng] [2024-05-18 01:37:39,822] [pool-1-thread-6] Initializing /data/ascb/514_9903.mrc: 
   [testng] 01:37:39,822 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
   [testng] 01:37:39,822 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:37:39,823 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-18_01-37-39.log]
   [testng] 01:37:39,823 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1516e912 - End of configuration.
   [testng] [2024-05-18 01:37:39,843] [pool-1-thread-5] Initializing /data/jcb/thyl-apr23-4.rec: 
   [testng] 01:37:39,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
   [testng] 01:37:39,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:37:39,844 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-18_01-37-39.log]
   [testng] 01:37:39,844 |-INFO in ch.qos.logback.core.sift.SiftProcessor@456fdaeb - End of configuration.
   [testng] [2024-05-18 01:37:39,864] [pool-1-thread-4] Initializing /data/jcb/thylakoid5.rec: 
   [testng] 01:37:39,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
   [testng] 01:37:39,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:37:39,865 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-18_01-37-39.log]
   [testng] 01:37:39,865 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2dcfbd23 - End of configuration.
   [testng] [2024-05-18 01:37:39,881] [pool-1-thread-3] Initializing /data/dan/one.mrc: 
   [testng] 01:37:39,882 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
   [testng] 01:37:39,882 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:37:39,882 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-18_01-37-39.log]
   [testng] 01:37:39,883 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43cde3e7 - End of configuration.
   [testng] [2024-05-18 01:37:39,907] [pool-1-thread-2] Initializing /data/ascb/cfa1071.mrc: 
   [testng] 01:37:39,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
   [testng] 01:37:39,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:37:39,908 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-18_01-37-39.log]
   [testng] 01:37:39,909 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f464403 - End of configuration.
   [testng] [2024-05-18 01:37:41,505] [pool-1-thread-7] Initializing /data/ascb/c191ali.mrc: 
   [testng] [2024-05-18 01:37:41,515] [pool-1-thread-1] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: 
   [testng] [2024-05-18 01:37:41,523] [pool-1-thread-9] Initializing /data/dan/three.mrc: 
   [testng] [2024-05-18 01:37:41,533] [pool-1-thread-8] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: 
   [testng] [2024-05-18 01:37:41,543] [pool-1-thread-5] Initializing /data/ticket-10073/wtjoin4.rec: 
   [testng] [2024-05-18 01:37:41,552] [pool-1-thread-12] Initializing /data/strand/Series1_A.mrc: 
   [testng] [2024-05-18 01:37:41,562] [pool-1-thread-4] Initializing /data/samples/1160.mrc: 
   [testng] [2024-05-18 01:37:41,847] [pool-1-thread-3] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc: 
   [testng] 
   [testng] ===============================================
   [testng] Bio-Formats software test suite
   [testng] Total tests run: 1060, Failures: 0, Skips: 0
   [testng] ===============================================
   [testng] 

BUILD SUCCESSFUL
Total time: 14 seconds
Finished: SUCCESS