Skip to content

Console Output

Started by upstream project "BIOFORMATS-test-repo" build number 250
originally caused by:
 Started by upstream project "Trigger" build number 274
 originally caused by:
  Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4
[BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins16952628676875830727.sh
+ '[' jpeg2000 = slidebook ']'
++ date +%u
+ '[' 6 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_39472_merge_ci -v /uod/idr/repos/curated/jpeg2000:/data -v /uod/idr-scratch/merge-ci/curated/jpeg2000:/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] 05:53:58,693 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
   [testng] 05:53:58,695 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service.
   [testng] 05:53:58,695 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 05:53:58,696 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 05:53:58,696 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
   [testng] 05:53:58,696 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
   [testng] 05:53:58,697 |-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] 05:53:58,697 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 05:53:58,697 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 05:53:58,698 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
   [testng] 05:53:58,698 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
   [testng] 05:53:58,698 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
   [testng] 05:53:58,855 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
   [testng] 05:53:58,855 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
   [testng] 05:53:58,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
   [testng] 05:53:58,876 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
   [testng] 05:53:58,881 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
   [testng] 05:53:58,881 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
   [testng] 05:53:58,881 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
   [testng] 05:53:58,881 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
   [testng] 05:53:58,881 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration.
   [testng] 05:53:58,882 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point
   [testng] 05:53:58,882 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 185 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
   [testng] [2024-11-09 05:53:58,890] [main] java.version = 11.0.16
   [testng] 05:53:58,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
   [testng] 05:53:58,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 05:53:58,933 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-09_05-53-58.log]
   [testng] 05:53:58,934 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration.
   [testng] [2024-11-09 05:53:58,936] [main] testng.directory = /data
   [testng] [2024-11-09 05:53:58,936] [main] testng.configDirectory = /config
   [testng] [2024-11-09 05:53:58,945] [main] testng.multiplier = 1.0
   [testng] [2024-11-09 05:53:58,946] [main] testng.in-memory = false
   [testng] [2024-11-09 05:53:58,946] [main] testng.allow-missing = false
   [testng] [2024-11-09 05:53:58,946] [main] user.language = en
   [testng] [2024-11-09 05:53:58,946] [main] user.country = ${user.country}
   [testng] [2024-11-09 05:53:58,946] [main] Maximum heap size = 15360 MB
   [testng] Scanning for files...
   [testng] [2024-11-09 05:54:39,448] [main] ----------------------------------------
   [testng] [2024-11-09 05:54:39,448] [main] Total files: 31
   [testng] [2024-11-09 05:54:39,448] [main] Scan time: 40.501 s (1306 ms/file)
   [testng] [2024-11-09 05:54:39,448] [main] ----------------------------------------
   [testng] Building list of tests...
   [testng] Ready to test 30 files
   [testng] [TestNG] Running:
   [testng]   Bio-Formats software test suite
   [testng] 
   [testng] [2024-11-09 05:55:23,573] [pool-1-thread-1] Initializing /data/venu/Multichannel 3a.jpg: 
   [testng] 05:55:23,573 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
   [testng] 05:55:23,574 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 05:55:23,575 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-09_05-55-23.log]
   [testng] 05:55:23,576 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1513eab0 - End of configuration.
   [testng] [2024-11-09 05:55:23,851] [pool-1-thread-12] Initializing /data/mike/LCM-4-3-color-cleaned.jp2: 
   [testng] 05:55:23,851 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
   [testng] 05:55:23,851 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 05:55:23,853 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-09_05-55-23.log]
   [testng] 05:55:23,853 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ba70882 - End of configuration.
   [testng] [2024-11-09 05:55:25,034] [pool-1-thread-11] Initializing /data/david/multichannel-2d test-non MBF-type.jp2: 
   [testng] 05:55:25,035 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
   [testng] 05:55:25,035 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 05:55:25,035 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-09_05-55-25.log]
   [testng] 05:55:25,036 |-INFO in ch.qos.logback.core.sift.SiftProcessor@182f1328 - End of configuration.
   [testng] [2024-11-09 05:55:26,179] [pool-1-thread-10] Initializing /data/angel/002_L050071_32_01_09_x2.jp2: 
   [testng] 05:55:26,179 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
   [testng] 05:55:26,180 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 05:55:26,180 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-09_05-55-26.log]
   [testng] 05:55:26,180 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7daa9f14 - End of configuration.
   [testng] [2024-11-09 05:55:27,435] [pool-1-thread-9] Initializing /data/david/C1R1_FOS.jp2: 
   [testng] 05:55:27,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
   [testng] 05:55:27,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 05:55:27,436 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-09_05-55-27.log]
   [testng] 05:55:27,436 |-INFO in ch.qos.logback.core.sift.SiftProcessor@560a82fe - End of configuration.
   [testng] [2024-11-09 05:55:28,525] [pool-1-thread-8] Initializing /data/vikram/Captured 3.jp2: 
   [testng] 05:55:28,525 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
   [testng] 05:55:28,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 05:55:28,526 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-09_05-55-28.log]
   [testng] 05:55:28,526 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4334ba - End of configuration.
   [testng] [2024-11-09 05:55:29,660] [pool-1-thread-7] Initializing /data/vikram/Captured 2.jp2: 
   [testng] 05:55:29,660 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
   [testng] 05:55:29,660 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 05:55:29,661 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-09_05-55-29.log]
   [testng] 05:55:29,661 |-INFO in ch.qos.logback.core.sift.SiftProcessor@736d55c - End of configuration.
   [testng] [2024-11-09 05:55:30,792] [pool-1-thread-6] Initializing /data/venu/Multichannel 3.jp2: 
   [testng] 05:55:30,792 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
   [testng] 05:55:30,792 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 05:55:30,793 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-09_05-55-30.log]
   [testng] 05:55:30,793 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1be21ebe - End of configuration.
   [testng] [2024-11-09 05:55:32,036] [pool-1-thread-5] Initializing /data/angel/052_L050071_56_x2hv.jp2: 
   [testng] 05:55:32,036 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
   [testng] 05:55:32,036 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 05:55:32,037 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-09_05-55-32.log]
   [testng] 05:55:32,037 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c692b2f - End of configuration.
   [testng] [2024-11-09 05:55:33,293] [pool-1-thread-4] Initializing /data/misc/clown-rgb.jpc: 
   [testng] 05:55:33,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
   [testng] 05:55:33,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 05:55:33,294 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-09_05-55-33.log]
   [testng] 05:55:33,294 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b48f2cf - End of configuration.
   [testng] [2024-11-09 05:55:34,447] [pool-1-thread-3] Initializing /data/frans/flower.jp2: 
   [testng] 05:55:34,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
   [testng] 05:55:34,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 05:55:34,448 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-09_05-55-34.log]
   [testng] 05:55:34,448 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58fe3d4a - End of configuration.
   [testng] [2024-11-09 05:55:35,537] [pool-1-thread-2] Initializing /data/david/000000_000001.jpx: 
   [testng] 05:55:35,537 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
   [testng] 05:55:35,538 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 05:55:35,538 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-09_05-55-35.log]
   [testng] 05:55:35,538 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ee7227f - End of configuration.
   [testng] [2024-11-09 05:55:43,702] [pool-1-thread-1] Initializing /data/mike/LCM4-1-cr10-cleaned.jp2: 
   [testng] [2024-11-09 05:55:45,918] [pool-1-thread-4] Initializing /data/david/multichannel-2d test.jp2: 
   [testng] [2024-11-09 05:55:47,043] [pool-1-thread-8] Initializing /data/misc/clown-rgb.jp2: 
   [testng] [2024-11-09 05:55:48,182] [pool-1-thread-7] Initializing /data/david/multichannel-3d-non-MBF-trial-2.jpx: 
   [testng] [2024-11-09 05:55:54,878] [pool-1-thread-2] Initializing /data/big-images/2kx2k.jpf: 
   [testng] [2024-11-09 05:55:58,029] [pool-1-thread-8] Initializing /data/big-images/4kx4k.jpf: 
   [testng] [2024-11-09 05:55:59,841] [pool-1-thread-12] Initializing /data/david/cy5-tph.jp2: 
   [testng] [2024-11-09 05:56:04,000] [pool-1-thread-10] Initializing /data/mike/LCM-4-3-color-cleaned.tiff: 
   [testng] [2024-11-09 05:56:06,846] [pool-1-thread-6] Initializing /data/david/multichannel-3d-MBF-type.jpx: 
   [testng] [2024-11-09 05:56:08,362] [pool-1-thread-1] Initializing /data/mike/LCM-4-3-color-cleaned-LOCI.tiff: 
   [testng] [2024-11-09 05:56:11,300] [pool-1-thread-3] Initializing /data/vikram/Captured 5.jp2: 
   [testng] [2024-11-09 05:56:12,749] [pool-1-thread-5] Initializing /data/vikram/Captured 4.jp2: 
   [testng] [2024-11-09 05:56:23,035] [pool-1-thread-3] Initializing /data/kraig/head.jp2: 
   [testng] [2024-11-09 05:56:24,547] [pool-1-thread-5] Initializing /data/aryeh/flour 12.jp2: 
   [testng] [2024-11-09 05:56:25,899] [pool-1-thread-2] Initializing /data/big-images/8kx8k.jpf: 
   [testng] [2024-11-09 05:56:27,037] [pool-1-thread-9] Initializing /data/misc/clown-rgb.jbig: 
   [testng] [2024-11-09 05:56:36,248] [pool-1-thread-1] Initializing /data/vikram/Captured 1.jp2: 
   [testng] [2024-11-09 05:56:37,480] [pool-1-thread-10] Initializing /data/mario/b0bCDME-0007_wB05_s1_z1_t1_cGFP_u001.jp2: 
   [testng] 
   [testng] ===============================================
   [testng] Bio-Formats software test suite
   [testng] Total tests run: 1590, Failures: 0, Skips: 0
   [testng] ===============================================
   [testng] 

BUILD SUCCESSFUL
Total time: 8 minutes 48 seconds
Finished: SUCCESS