Skip to content
[Jenkins]Jenkins
log in

Console Output

Started by upstream project "BIOFORMATS-test-repo" build number 221
originally caused by:
 Started by upstream project "Trigger" build number 248
 originally caused by:
  Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9
[BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins15013328395068349569.sh
+ '[' perkinelmer-operetta = slidebook ']'
++ date +%u
+ '[' 2 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_35063_merge_ci -v /uod/idr/repos/curated/perkinelmer-operetta:/data -v /uod/idr-scratch/merge-ci/curated/perkinelmer-operetta:/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] 02:14:37,110 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
   [testng] 02:14:37,112 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service.
   [testng] 02:14:37,112 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 02:14:37,113 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 02:14:37,113 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
   [testng] 02:14:37,114 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
   [testng] 02:14:37,114 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
   [testng] 02:14:37,114 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 02:14:37,115 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 02:14:37,115 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
   [testng] 02:14:37,115 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
   [testng] 02:14:37,116 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
   [testng] 02:14:37,298 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
   [testng] 02:14:37,298 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
   [testng] 02:14:37,320 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
   [testng] 02:14:37,320 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
   [testng] 02:14:37,326 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
   [testng] 02:14:37,326 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
   [testng] 02:14:37,326 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
   [testng] 02:14:37,327 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
   [testng] 02:14:37,327 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration.
   [testng] 02:14:37,328 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point
   [testng] 02:14:37,328 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 213 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
   [testng] [2024-10-15 02:14:37,337] [main] java.version = 11.0.16
   [testng] 02:14:37,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
   [testng] 02:14:37,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:14:37,383 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-15_02-14-37.log]
   [testng] 02:14:37,385 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration.
   [testng] [2024-10-15 02:14:37,387] [main] testng.directory = /data
   [testng] [2024-10-15 02:14:37,387] [main] testng.configDirectory = /config
   [testng] [2024-10-15 02:14:37,397] [main] testng.multiplier = 1.0
   [testng] [2024-10-15 02:14:37,398] [main] testng.in-memory = false
   [testng] [2024-10-15 02:14:37,399] [main] testng.allow-missing = false
   [testng] [2024-10-15 02:14:37,399] [main] user.language = en
   [testng] [2024-10-15 02:14:37,399] [main] user.country = ${user.country}
   [testng] [2024-10-15 02:14:37,399] [main] Maximum heap size = 15360 MB
   [testng] Scanning for files...
   [testng] [2024-10-15 02:40:22,107] [main] ----------------------------------------
   [testng] [2024-10-15 02:40:22,108] [main] Total files: 14663
   [testng] [2024-10-15 02:40:22,108] [main] Scan time: 1544.708 s (105 ms/file)
   [testng] [2024-10-15 02:40:22,108] [main] ----------------------------------------
   [testng] Building list of tests...
   [testng] Ready to test 16 files
   [testng] [TestNG] Running:
   [testng]   Bio-Formats software test suite
   [testng] 
   [testng] [2024-10-15 03:53:34,266] [pool-1-thread-1] Initializing /data/pki/DataSet/dec61bf8-5ca8-415a-8639-b75bf59ca47c/images/index.xml: 
   [testng] 03:53:34,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
   [testng] 03:53:34,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 03:53:34,269 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-15_03-53-34.log]
   [testng] 03:53:34,269 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3509b72e - End of configuration.
   [testng] [2024-10-15 03:53:53,246] [pool-1-thread-12] Initializing /data/samples/new-phenix/artificial-v6/Hiplex_run1_cycle1_MsPos/Index.idx.xml: 
   [testng] 03:53:53,246 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
   [testng] 03:53:53,246 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 03:53:53,247 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-15_03-53-53.log]
   [testng] 03:53:53,247 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2231d09e - End of configuration.
   [testng] [2024-10-15 03:56:35,887] [pool-1-thread-11] Initializing /data/public/idr0034/HipSci Experiment 10 Plate 1__2014-08-21T17_57_35-Measurement1/Images/Index.idx.xml: 
   [testng] 03:56:35,888 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
   [testng] 03:56:35,888 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 03:56:35,888 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-15_03-56-35.log]
   [testng] 03:56:35,889 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b344710 - End of configuration.
   [testng] [2024-10-15 04:02:08,208] [pool-1-thread-10] Initializing /data/samples/no-first-series/Index.idx.xml: 
   [testng] 04:02:08,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
   [testng] 04:02:08,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:02:08,209 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-15_04-02-08.log]
   [testng] 04:02:08,209 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4798003 - End of configuration.
   [testng] [2024-10-15 04:02:15,748] [pool-1-thread-9] Initializing /data/qa-17826/JLM-20170801-Operetta/Index.idx.xml: 
   [testng] 04:02:15,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
   [testng] 04:02:15,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:02:15,749 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-15_04-02-15.log]
   [testng] 04:02:15,749 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a60f162 - End of configuration.
   [testng] [2024-10-15 04:02:25,082] [pool-1-thread-8] Initializing /data/hms/ryang_skbr3_p1__2012-07-10T15_24_30-Measurement1/Images/Index.idx.xml: 
   [testng] 04:02:25,082 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
   [testng] 04:02:25,082 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:02:25,083 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-15_04-02-25.log]
   [testng] 04:02:25,083 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2bddc74e - End of configuration.
   [testng] [2024-10-15 04:02:31,734] [pool-1-thread-7] Initializing /data/public/omer/006P_M3/006P_M3_overview_fields.png: 
   [testng] 04:02:31,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
   [testng] 04:02:31,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:02:31,735 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-15_04-02-31.log]
   [testng] 04:02:31,736 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b3587f8 - End of configuration.
   [testng] [2024-10-15 04:02:32,516] [pool-1-thread-6] Initializing /data/public/omer/006P_M3/006P_M3_overview.png: 
   [testng] 04:02:32,516 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
   [testng] 04:02:32,516 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:02:32,517 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-15_04-02-32.log]
   [testng] 04:02:32,517 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2edf00c - End of configuration.
   [testng] [2024-10-15 04:02:33,389] [pool-1-thread-5] Initializing /data/public/omer/006P_M3/006P__2017-08-19T12_42_59-Measurement 3/Images/Index.idx.xml: 
   [testng] 04:02:33,389 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
   [testng] 04:02:33,389 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:02:33,390 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-15_04-02-33.log]
   [testng] 04:02:33,390 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ac839d - End of configuration.
   [testng] [2024-10-15 04:05:06,902] [pool-1-thread-4] Initializing /data/stephen/Plate 1(2)__2011-09-29T23_50_20-Measurement1/Images/Index.idx.xml: 
   [testng] 04:05:06,903 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
   [testng] 04:05:06,903 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:05:06,903 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-15_04-05-06.log]
   [testng] 04:05:06,904 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6316fc7 - End of configuration.
   [testng] [2024-10-15 04:05:21,112] [pool-1-thread-3] Initializing /data/samples/smaller-xy/Index.idx.xml: 
   [testng] 04:05:21,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
   [testng] 04:05:21,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:05:21,113 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-15_04-05-21.log]
   [testng] 04:05:21,113 |-INFO in ch.qos.logback.core.sift.SiftProcessor@727340a3 - End of configuration.
   [testng] [2024-10-15 04:05:35,218] [pool-1-thread-2] Initializing /data/public/zenodo-7841360/Hoechst__2023-03-07T10_17_54-Measurement 2/Images/Index.idx.xml: 
   [testng] 04:05:35,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
   [testng] 04:05:35,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:05:35,219 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-15_04-05-35.log]
   [testng] 04:05:35,219 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4cbf6215 - End of configuration.
   [testng] [2024-10-15 04:05:55,117] [pool-1-thread-7] Initializing /data/samples/new-phenix/original/Hiplex_run1_cycle1_MsPos/Index.idx.xml: 
   [testng] [2024-10-15 04:08:42,989] [pool-1-thread-6] Initializing /data/pki/Export/HRMNY-13786__2021-11-23T13_44_30-Measurement 3/Images/Index.xml: 
   [testng] [2024-10-15 04:09:50,998] [pool-1-thread-2] Initializing /data/samples/32-bit-file/Index.idx.xml: 
   [testng] [2024-10-15 04:11:07,380] [pool-1-thread-10] Initializing /data/stephen/P004-CC Edu-pHH3__2009-02-03T17_36_29-Measurement1/Images/Index.idx.xml: 
time="2024-10-15T06:00:37Z" level=error msg="error waiting for container: unexpected EOF"
Build step 'Execute shell' marked build as failure
Finished: FAILURE