Skip to content
[Jenkins]Jenkins
log in

Console Output

Started by upstream project "BIOFORMATS-test-repo" build number 120
originally caused by:
 Started by upstream project "Trigger" build number 137
 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/jenkins11130919569650444470.sh
+ '[' mrc = slidebook ']'
++ date +%u
+ '[' 7 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_18729_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] 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] 01:35:51,876 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
   [testng] 01:35:51,877 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service.
   [testng] 01:35:51,877 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 01:35:51,878 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 01:35:51,878 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
   [testng] 01:35:51,879 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
   [testng] 01:35:51,879 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
   [testng] 01:35:51,879 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 01:35:51,879 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 01:35:51,880 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
   [testng] 01:35:51,880 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
   [testng] 01:35:51,880 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
   [testng] 01:35:52,040 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
   [testng] 01:35:52,040 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
   [testng] 01:35:52,062 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
   [testng] 01:35:52,062 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
   [testng] 01:35:52,068 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
   [testng] 01:35:52,068 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
   [testng] 01:35:52,068 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
   [testng] 01:35:52,069 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
   [testng] 01:35:52,069 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration.
   [testng] 01:35:52,069 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point
   [testng] 01:35:52,070 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 190 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
   [testng] [2024-07-14 01:35:52,078] [main] java.version = 17.0.2
   [testng] 01:35:52,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
   [testng] 01:35:52,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:35:52,122 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-14_01-35-52.log]
   [testng] 01:35:52,123 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration.
   [testng] [2024-07-14 01:35:52,125] [main] testng.directory = /data
   [testng] [2024-07-14 01:35:52,125] [main] testng.configDirectory = /config
   [testng] [2024-07-14 01:35:52,134] [main] testng.multiplier = 1.0
   [testng] [2024-07-14 01:35:52,135] [main] testng.in-memory = false
   [testng] [2024-07-14 01:35:52,135] [main] testng.allow-missing = false
   [testng] [2024-07-14 01:35:52,135] [main] user.language = en
   [testng] [2024-07-14 01:35:52,135] [main] user.country = ${user.country}
   [testng] [2024-07-14 01:35:52,135] [main] Maximum heap size = 15360 MB
   [testng] Scanning for files...
   [testng] [2024-07-14 01:35:53,708] [main] ----------------------------------------
   [testng] [2024-07-14 01:35:53,709] [main] Total files: 20
   [testng] [2024-07-14 01:35:53,709] [main] Scan time: 1.573 s (78 ms/file)
   [testng] [2024-07-14 01:35:53,709] [main] ----------------------------------------
   [testng] Building list of tests...
   [testng] Ready to test 20 files
   [testng] [TestNG] Running:
   [testng]   Bio-Formats software test suite
   [testng] 
   [testng] [2024-07-14 01:35:54,135] [pool-1-thread-1] Initializing /data/ticket-10073/wtjoin4.rec: 
   [testng] 01:35:54,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
   [testng] 01:35:54,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:35:54,136 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-14_01-35-54.log]
   [testng] 01:35:54,137 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9906c5b - End of configuration.
   [testng] [2024-07-14 01:35:54,157] [pool-1-thread-12] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: 
   [testng] 01:35:54,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
   [testng] 01:35:54,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:35:54,171 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-14_01-35-54.log]
   [testng] 01:35:54,172 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35da5f75 - End of configuration.
   [testng] [2024-07-14 01:35:54,199] [pool-1-thread-11] Initializing /data/dan/three.mrc: 
   [testng] 01:35:54,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
   [testng] 01:35:54,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:35:54,201 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-14_01-35-54.log]
   [testng] 01:35:54,202 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1fe6bb8d - End of configuration.
   [testng] [2024-07-14 01:35:54,218] [pool-1-thread-10] Initializing /data/ascb/cfa1071.mrc: 
   [testng] 01:35:54,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
   [testng] 01:35:54,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:35:54,219 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-14_01-35-54.log]
   [testng] 01:35:54,219 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2aeb0854 - End of configuration.
   [testng] [2024-07-14 01:35:54,232] [pool-1-thread-9] Initializing /data/bioformats2raw-198/test_uint8.mrc: 
   [testng] 01:35:54,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
   [testng] 01:35:54,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:35:54,233 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-14_01-35-54.log]
   [testng] 01:35:54,233 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20ca8ff4 - End of configuration.
   [testng] [2024-07-14 01:35:54,251] [pool-1-thread-8] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: 
   [testng] 01:35:54,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
   [testng] 01:35:54,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:35:54,252 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-14_01-35-54.log]
   [testng] 01:35:54,252 |-INFO in ch.qos.logback.core.sift.SiftProcessor@281cba5d - End of configuration.
   [testng] [2024-07-14 01:35:54,263] [pool-1-thread-7] Initializing /data/strand/Series1_A.mrc: 
   [testng] 01:35:54,264 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
   [testng] 01:35:54,264 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:35:54,264 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-14_01-35-54.log]
   [testng] 01:35:54,265 |-INFO in ch.qos.logback.core.sift.SiftProcessor@254e350f - End of configuration.
   [testng] [2024-07-14 01:35:54,289] [pool-1-thread-6] Initializing /data/jcb/thylakoid5.rec: 
   [testng] 01:35:54,289 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
   [testng] 01:35:54,289 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:35:54,290 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-14_01-35-54.log]
   [testng] 01:35:54,290 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57034d4 - End of configuration.
   [testng] [2024-07-14 01:35:54,333] [pool-1-thread-5] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: 
   [testng] 01:35:54,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
   [testng] 01:35:54,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:35:54,334 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-14_01-35-54.log]
   [testng] 01:35:54,334 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c364cec - End of configuration.
   [testng] [2024-07-14 01:35:54,348] [pool-1-thread-4] Initializing /data/ascb/c191.st: 
   [testng] 01:35:54,348 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
   [testng] 01:35:54,348 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:35:54,349 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-14_01-35-54.log]
   [testng] 01:35:54,350 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d5c5f96 - End of configuration.
   [testng] [2024-07-14 01:35:54,364] [pool-1-thread-3] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: 
   [testng] 01:35:54,364 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
   [testng] 01:35:54,364 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:35:54,365 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-14_01-35-54.log]
   [testng] 01:35:54,366 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e83da82 - End of configuration.
   [testng] [2024-07-14 01:35:54,380] [pool-1-thread-2] Initializing /data/samples/golgi.mrc: 
   [testng] 01:35:54,380 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
   [testng] 01:35:54,380 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:35:54,381 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-14_01-35-54.log]
   [testng] 01:35:54,381 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27b7fd8d - End of configuration.
   [testng] [2024-07-14 01:35:55,717] [pool-1-thread-9] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc: 
   [testng] [2024-07-14 01:35:55,731] [pool-1-thread-12] Initializing /data/jcb/thyl-apr23-4.rec: 
   [testng] [2024-07-14 01:35:55,745] [pool-1-thread-3] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc: 
   [testng] [2024-07-14 01:35:55,763] [pool-1-thread-5] Initializing /data/dan/two.mrc: 
   [testng] [2024-07-14 01:35:55,781] [pool-1-thread-8] Initializing /data/ascb/514_9903.mrc: 
   [testng] [2024-07-14 01:35:55,796] [pool-1-thread-2] Initializing /data/ascb/c191ali.mrc: 
   [testng] [2024-07-14 01:35:55,812] [pool-1-thread-4] Initializing /data/samples/1160.mrc: 
   [testng] [2024-07-14 01:35:55,828] [pool-1-thread-6] Initializing /data/dan/one.mrc: 
   [testng] 
   [testng] ===============================================
   [testng] Bio-Formats software test suite
   [testng] Total tests run: 1060, Failures: 0, Skips: 0
   [testng] ===============================================
   [testng] 

BUILD SUCCESSFUL
Total time: 12 seconds
Finished: SUCCESS