Skip to content
[Jenkins]Jenkins
log in

Console Output

Started by upstream project "BIOFORMATS-test-repo" build number 231
originally caused by:
 Started by upstream project "Trigger" build number 256
 originally caused by:
  Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8
[BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins13221582392961183982.sh
+ '[' imspector = slidebook ']'
++ date +%u
+ '[' 2 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_36321_merge_ci -v /uod/idr/repos/curated/imspector:/data -v /uod/idr-scratch/merge-ci/curated/imspector:/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] 04:17:48,130 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
   [testng] 04:17:48,131 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service.
   [testng] 04:17:48,131 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 04:17:48,132 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 04:17:48,133 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
   [testng] 04:17:48,133 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
   [testng] 04:17:48,133 |-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] 04:17:48,133 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 04:17:48,134 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 04:17:48,134 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
   [testng] 04:17:48,135 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
   [testng] 04:17:48,135 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
   [testng] 04:17:48,297 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
   [testng] 04:17:48,297 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
   [testng] 04:17:48,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
   [testng] 04:17:48,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
   [testng] 04:17:48,324 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
   [testng] 04:17:48,324 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
   [testng] 04:17:48,324 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
   [testng] 04:17:48,325 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
   [testng] 04:17:48,325 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration.
   [testng] 04:17:48,326 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point
   [testng] 04:17:48,326 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 192 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
   [testng] [2024-10-22 04:17:48,334] [main] java.version = 11.0.16
   [testng] 04:17:48,337 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
   [testng] 04:17:48,337 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:17:48,382 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-22_04-17-48.log]
   [testng] 04:17:48,384 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration.
   [testng] [2024-10-22 04:17:48,386] [main] testng.directory = /data
   [testng] [2024-10-22 04:17:48,386] [main] testng.configDirectory = /config
   [testng] [2024-10-22 04:17:48,395] [main] testng.multiplier = 1.0
   [testng] [2024-10-22 04:17:48,396] [main] testng.in-memory = false
   [testng] [2024-10-22 04:17:48,397] [main] testng.allow-missing = false
   [testng] [2024-10-22 04:17:48,397] [main] user.language = en
   [testng] [2024-10-22 04:17:48,397] [main] user.country = ${user.country}
   [testng] [2024-10-22 04:17:48,397] [main] Maximum heap size = 15360 MB
   [testng] Scanning for files...
   [testng] [2024-10-22 04:18:10,092] [main] ----------------------------------------
   [testng] [2024-10-22 04:18:10,092] [main] Total files: 29
   [testng] [2024-10-22 04:18:10,092] [main] Scan time: 21.695 s (748 ms/file)
   [testng] [2024-10-22 04:18:10,093] [main] ----------------------------------------
   [testng] Building list of tests...
   [testng] Ready to test 28 files
   [testng] [TestNG] Running:
   [testng]   Bio-Formats software test suite
   [testng] 
   [testng] [2024-10-22 04:18:33,268] [pool-1-thread-1] Initializing /data/qa-4929/OMERO data/01 - 27hpf_f2-GFP-wt1b+rfp-flk1 - 3channel-z-stack.msr: 
   [testng] 04:18:33,269 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
   [testng] 04:18:33,269 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:18:33,271 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-22_04-18-33.log]
   [testng] 04:18:33,272 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f3a5b03 - End of configuration.
   [testng] [2024-10-22 04:18:33,830] [pool-1-thread-12] Initializing /data/qa-7658/Document1_13-09-25.msr: 
   [testng] 04:18:33,830 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
   [testng] 04:18:33,830 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:18:33,831 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-22_04-18-33.log]
   [testng] 04:18:33,831 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2937bd26 - End of configuration.
   [testng] [2024-10-22 04:18:34,403] [pool-1-thread-11] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_z-stack_FLIM_TDC_C0.ome.tif: 
   [testng] 04:18:34,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
   [testng] 04:18:34,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:18:34,403 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-22_04-18-34.log]
   [testng] 04:18:34,404 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21c2ef8c - End of configuration.
   [testng] [2024-10-22 04:18:35,358] [pool-1-thread-10] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel single slice.msr: 
   [testng] 04:18:35,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
   [testng] 04:18:35,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:18:35,359 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-22_04-18-35.log]
   [testng] 04:18:35,360 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d4020b - End of configuration.
   [testng] [2024-10-22 04:18:35,930] [pool-1-thread-9] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel Zstack.msr: 
   [testng] 04:18:35,930 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
   [testng] 04:18:35,930 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:18:35,931 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-22_04-18-35.log]
   [testng] 04:18:35,931 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d02d744 - End of configuration.
   [testng] [2024-10-22 04:18:36,481] [pool-1-thread-8] Initializing /data/qa-7702/trim- scope msr z-stacks/02 -  500x500x105_1046x1046x57_1.875um_steps/02 -  500x500x105_1046x1046x57_1_875um_steps_11-34-02_PMT - PMT [PMT1] _C0.ome.tif: 
   [testng] 04:18:36,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
   [testng] 04:18:36,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:18:36,481 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-22_04-18-36.log]
   [testng] 04:18:36,482 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a7a20c - End of configuration.
   [testng] [2024-10-22 04:18:38,742] [pool-1-thread-7] Initializing /data/qa-7992/NegativeArraySizeException_small.msr: 
   [testng] 04:18:38,742 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
   [testng] 04:18:38,742 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:18:38,743 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-22_04-18-38.log]
   [testng] 04:18:38,743 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d2b4932 - End of configuration.
   [testng] [2024-10-22 04:18:39,643] [pool-1-thread-6] Initializing /data/qa-7992/ArrayIndexOutOfBoundsException.msr: 
   [testng] 04:18:39,644 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
   [testng] 04:18:39,644 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:18:39,644 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-22_04-18-39.log]
   [testng] 04:18:39,645 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34eb5aff - End of configuration.
   [testng] [2024-10-22 04:18:40,459] [pool-1-thread-5] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning.msr: 
   [testng] 04:18:40,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
   [testng] 04:18:40,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:18:40,460 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-22_04-18-40.log]
   [testng] 04:18:40,460 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17174873 - End of configuration.
   [testng] [2024-10-22 04:18:41,137] [pool-1-thread-4] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel single slice 4 tiles.msr: 
   [testng] 04:18:41,137 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
   [testng] 04:18:41,137 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:18:41,137 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-22_04-18-41.log]
   [testng] 04:18:41,138 |-INFO in ch.qos.logback.core.sift.SiftProcessor@359fddf3 - End of configuration.
   [testng] [2024-10-22 04:18:41,741] [pool-1-thread-3] Initializing /data/qa-27309/181109_e3_cut.msr: 
   [testng] 04:18:41,741 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
   [testng] 04:18:41,741 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:18:41,741 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-22_04-18-41.log]
   [testng] 04:18:41,742 |-INFO in ch.qos.logback.core.sift.SiftProcessor@503a869e - End of configuration.
   [testng] [2024-10-22 04:18:42,302] [pool-1-thread-2] Initializing /data/qa-17102/2 channels FLIM time series.msr: 
   [testng] 04:18:42,303 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
   [testng] 04:18:42,303 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 04:18:42,303 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-22_04-18-42.log]
   [testng] 04:18:42,303 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7cf41a0f - End of configuration.
   [testng] [2024-10-22 04:18:49,462] [pool-1-thread-3] Initializing /data/qa-7936/02 - not working.msr: 
   [testng] [2024-10-22 04:18:49,838] [pool-1-thread-10] Initializing /data/qa-7992/IllegalArgumentException.msr: 
   [testng] [2024-10-22 04:18:50,276] [pool-1-thread-2] Initializing /data/qa-7702/trim- scope msr z-stacks/02 -  500x500x105_1046x1046x57_1.875um_steps.msr: 
   [testng] [2024-10-22 04:18:50,678] [pool-1-thread-6] Initializing /data/qa-4929/OMERO data/01 - urea_irf_image_TCSPC-data.msr: 
   [testng] [2024-10-22 04:18:51,162] [pool-1-thread-1] Initializing /data/qa-17102/1 channel binning 4 time series.msr: 
   [testng] [2024-10-22 04:18:51,734] [pool-1-thread-7] Initializing /data/qa-7936/01 - working.msr: 
   [testng] [2024-10-22 04:18:52,597] [pool-1-thread-12] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel Zstack.msr: 
   [testng] [2024-10-22 04:18:53,434] [pool-1-thread-5] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning_12-08-53_TCSPC_C0.ome.tif: 
   [testng] [2024-10-22 04:18:54,589] [pool-1-thread-9] Initializing /data/paul/msr files - Paul Thomas UEA/Lifetime file.msr: 
   [testng] [2024-10-22 04:18:54,972] [pool-1-thread-4] Initializing /data/qa-11369/02 - 70 - 1 - tp1 - x16 TCSPC.msr: 
   [testng] [2024-10-22 04:18:56,440] [pool-1-thread-11] Initializing /data/qa-9468/HPDR10467U-40-VD0191-red-100pc-without-tube.msr: 
   [testng] [2024-10-22 04:18:59,606] [pool-1-thread-9] Initializing /data/qa-11369/01 - 770nm FITC - HybridPMT.msr: 
   [testng] [2024-10-22 04:19:00,522] [pool-1-thread-10] Initializing /data/qa-17102/2 channels FLIM z stack.msr: 
   [testng] [2024-10-22 04:19:01,297] [pool-1-thread-3] Initializing /data/qa-17102/1 channel binning 8 time series.msr: 
   [testng] [2024-10-22 04:19:01,689] [pool-1-thread-6] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_FLIM_z-stack_1.msr: 
   [testng] [2024-10-22 04:19:02,094] [pool-1-thread-4] Initializing /data/qa-7936/z-TC - for LOCI.msr: 
   [testng] 
   [testng] ===============================================
   [testng] Bio-Formats software test suite
   [testng] Total tests run: 1484, Failures: 0, Skips: 0
   [testng] ===============================================
   [testng] 

BUILD SUCCESSFUL
Total time: 1 minute 26 seconds
Finished: SUCCESS