Skip to content
[Jenkins]Jenkins
log in

Console Output

Started by upstream project "BIOFORMATS-test-repo" build number 301
originally caused by:
 Started by upstream project "Trigger" build number 323
 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/jenkins520812024005948823.sh
+ '[' perkinelmer-operetta = slidebook ']'
++ date +%u
+ '[' 6 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_47602_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] 01:09:49,293 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
   [testng] 01:09:49,295 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service.
   [testng] 01:09:49,295 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 01:09:49,296 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 01:09:49,297 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
   [testng] 01:09:49,297 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
   [testng] 01:09:49,298 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
   [testng] 01:09:49,298 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 01:09:49,298 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 01:09:49,299 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
   [testng] 01:09:49,299 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
   [testng] 01:09:49,300 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
   [testng] 01:09:49,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
   [testng] 01:09:49,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
   [testng] 01:09:49,504 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
   [testng] 01:09:49,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
   [testng] 01:09:49,511 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
   [testng] 01:09:49,511 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
   [testng] 01:09:49,511 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
   [testng] 01:09:49,511 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
   [testng] 01:09:49,511 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration.
   [testng] 01:09:49,513 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point
   [testng] 01:09:49,514 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 215 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
   [testng] [2024-12-28 01:09:49,529] [main] java.version = 11.0.16
   [testng] 01:09:49,534 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
   [testng] 01:09:49,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:09:49,601 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-28_01-09-49.log]
   [testng] 01:09:49,603 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration.
   [testng] [2024-12-28 01:09:49,606] [main] testng.directory = /data
   [testng] [2024-12-28 01:09:49,606] [main] testng.configDirectory = /config
   [testng] [2024-12-28 01:09:49,616] [main] testng.multiplier = 1.0
   [testng] [2024-12-28 01:09:49,618] [main] testng.in-memory = false
   [testng] [2024-12-28 01:09:49,618] [main] testng.allow-missing = false
   [testng] [2024-12-28 01:09:49,618] [main] user.language = en
   [testng] [2024-12-28 01:09:49,618] [main] user.country = ${user.country}
   [testng] [2024-12-28 01:09:49,618] [main] Maximum heap size = 15360 MB
   [testng] Scanning for files...
   [testng] [2024-12-28 01:31:28,288] [main] ----------------------------------------
   [testng] [2024-12-28 01:31:28,289] [main] Total files: 14681
   [testng] [2024-12-28 01:31:28,289] [main] Scan time: 1298.67 s (88 ms/file)
   [testng] [2024-12-28 01:31:28,289] [main] ----------------------------------------
   [testng] Building list of tests...
   [testng] Ready to test 17 files
   [testng] [TestNG] Running:
   [testng]   Bio-Formats software test suite
   [testng] 
   [testng] [2024-12-28 02:13:05,283] [pool-1-thread-1] Initializing /data/samples/smaller-xy/Index.idx.xml: 
   [testng] 02:13:05,284 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
   [testng] 02:13:05,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:13:05,286 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-28_02-13-05.log]
   [testng] 02:13:05,287 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41f6af36 - End of configuration.
   [testng] [2024-12-28 02:13:07,271] [pool-1-thread-12] Initializing /data/samples/no-first-series/Index.idx.xml: 
   [testng] 02:13:07,271 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
   [testng] 02:13:07,271 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:13:07,272 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-28_02-13-07.log]
   [testng] 02:13:07,272 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b2cd835 - End of configuration.
   [testng] [2024-12-28 02:13:09,258] [pool-1-thread-11] Initializing /data/pki/Export/HRMNY-13786__2021-11-23T13_44_30-Measurement 3/Images/Index.xml: 
   [testng] 02:13:09,258 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
   [testng] 02:13:09,259 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:13:09,259 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-28_02-13-09.log]
   [testng] 02:13:09,260 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32311b7c - End of configuration.
   [testng] [2024-12-28 02:13:11,826] [pool-1-thread-10] Initializing /data/stephen/P004-CC Edu-pHH3__2009-02-03T17_36_29-Measurement1/Images/Index.idx.xml: 
   [testng] 02:13:11,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
   [testng] 02:13:11,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:13:11,827 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-28_02-13-11.log]
   [testng] 02:13:11,828 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e106129 - End of configuration.
   [testng] [2024-12-28 02:13:14,966] [pool-1-thread-9] Initializing /data/samples/extra-directories/Index.idx.xml: 
   [testng] 02:13:14,966 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
   [testng] 02:13:14,966 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:13:14,966 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-28_02-13-14.log]
   [testng] 02:13:14,967 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e543b26 - End of configuration.
   [testng] [2024-12-28 02:13:17,315] [pool-1-thread-8] Initializing /data/public/omer/006P_M3/006P_M3_overview.png: 
   [testng] 02:13:17,315 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
   [testng] 02:13:17,315 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:13:17,316 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-28_02-13-17.log]
   [testng] 02:13:17,316 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7fabdbdb - End of configuration.
   [testng] [2024-12-28 02:13:17,420] [pool-1-thread-7] Initializing /data/public/zenodo-7841360/Hoechst__2023-03-07T10_17_54-Measurement 2/Images/Index.idx.xml: 
   [testng] 02:13:17,420 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
   [testng] 02:13:17,420 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:13:17,421 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-28_02-13-17.log]
   [testng] 02:13:17,421 |-INFO in ch.qos.logback.core.sift.SiftProcessor@139d3c11 - End of configuration.
   [testng] [2024-12-28 02:13:18,816] [pool-1-thread-6] Initializing /data/public/idr0034/HipSci Experiment 10 Plate 1__2014-08-21T17_57_35-Measurement1/Images/Index.idx.xml: 
   [testng] 02:13:18,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
   [testng] 02:13:18,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:13:18,817 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-28_02-13-18.log]
   [testng] 02:13:18,817 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3986cf3f - End of configuration.
   [testng] [2024-12-28 02:14:05,881] [pool-1-thread-5] Initializing /data/public/omer/006P_M3/006P_M3_overview_fields.png: 
   [testng] 02:14:05,881 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
   [testng] 02:14:05,881 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:14:05,882 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-28_02-14-05.log]
   [testng] 02:14:05,882 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1766af3e - End of configuration.
   [testng] [2024-12-28 02:14:05,946] [pool-1-thread-4] Initializing /data/pki/DataSet/dec61bf8-5ca8-415a-8639-b75bf59ca47c/images/index.xml: 
   [testng] 02:14:05,947 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
   [testng] 02:14:05,947 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:14:05,947 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-28_02-14-05.log]
   [testng] 02:14:05,948 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6cac6d3c - End of configuration.
   [testng] [2024-12-28 02:14:09,780] [pool-1-thread-3] Initializing /data/hms/ryang_skbr3_p1__2012-07-10T15_24_30-Measurement1/Images/Index.idx.xml: 
   [testng] 02:14:09,780 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
   [testng] 02:14:09,780 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:14:09,781 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-28_02-14-09.log]
   [testng] 02:14:09,781 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10087879 - End of configuration.
   [testng] [2024-12-28 02:14:13,287] [pool-1-thread-2] Initializing /data/stephen/Plate 1(2)__2011-09-29T23_50_20-Measurement1/Images/Index.idx.xml: 
   [testng] 02:14:13,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
   [testng] 02:14:13,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:14:13,288 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-28_02-14-13.log]
   [testng] 02:14:13,289 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c81718 - End of configuration.
   [testng] [2024-12-28 02:14:22,733] [pool-1-thread-8] Initializing /data/qa-17826/JLM-20170801-Operetta/Index.idx.xml: 
   [testng] [2024-12-28 02:14:26,594] [pool-1-thread-5] Initializing /data/public/omer/006P_M3/006P__2017-08-19T12_42_59-Measurement 3/Images/Index.idx.xml: 
   [testng] [2024-12-28 02:15:04,772] [pool-1-thread-7] Initializing /data/samples/32-bit-file/Index.idx.xml: 
   [testng] [2024-12-28 02:16:57,834] [pool-1-thread-12] Initializing /data/samples/new-phenix/artificial-v6/Hiplex_run1_cycle1_MsPos/Index.idx.xml: 
   [testng] [2024-12-28 02:17:16,048] [pool-1-thread-3] Initializing /data/samples/new-phenix/original/Hiplex_run1_cycle1_MsPos/Index.idx.xml: 
   [testng] 06:01:55,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
   [testng] 06:01:55,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 06:01:55,150 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-28_06-01-55.log]
   [testng] 06:01:55,151 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a6a011c - End of configuration.
   [testng] 06:36:10,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
   [testng] 06:36:10,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 06:36:10,964 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-28_06-36-10.log]
   [testng] 06:36:10,965 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37eeaf6f - End of configuration.
   [testng] 06:36:11,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
   [testng] 06:36:11,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 06:36:11,943 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-28_06-36-11.log]
   [testng] 06:36:11,943 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71caf94c - End of configuration.
   [testng] 06:36:39,501 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
   [testng] 06:36:39,501 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 06:36:39,502 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-28_06-36-39.log]
   [testng] 06:36:39,502 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39ef746 - End of configuration.
   [testng] 
   [testng] ===============================================
   [testng] Bio-Formats software test suite
   [testng] Total tests run: 901, Failures: 0, Skips: 0
   [testng] ===============================================
   [testng] 

BUILD SUCCESSFUL
Total time: 326 minutes 53 seconds
Finished: SUCCESS