Skip to content
[Jenkins]Jenkins
log in

Console Output

Started by upstream project "BIOFORMATS-test-repo" build number 45
originally caused by:
 Started by upstream project "Trigger" build number 52
 originally caused by:
  Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5
[BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins18111515860263847593.sh
+ '[' vectra-qptiff = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_6419_merge_ci -v /uod/idr/repos/curated/vectra-qptiff:/data -v /uod/idr-scratch/merge-ci/curated/vectra-qptiff:/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

test-automated:
   [testng] File leak detector installed
   [testng] 01:31:01,751 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
   [testng] 01:31:01,753 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service.
   [testng] 01:31:01,753 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 01:31:01,754 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 01:31:01,754 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
   [testng] 01:31:01,754 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
   [testng] 01:31:01,755 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
   [testng] 01:31:01,755 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 01:31:01,755 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 01:31:01,755 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
   [testng] 01:31:01,755 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
   [testng] 01:31:01,756 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
   [testng] 01:31:01,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
   [testng] 01:31:01,986 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
   [testng] 01:31:02,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
   [testng] 01:31:02,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
   [testng] 01:31:02,022 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
   [testng] 01:31:02,023 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
   [testng] 01:31:02,023 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
   [testng] 01:31:02,023 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
   [testng] 01:31:02,023 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration.
   [testng] 01:31:02,024 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point
   [testng] 01:31:02,024 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 269 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
   [testng] [2024-04-26 01:31:02,034] [main] java.version = 1.8.0_342
   [testng] 01:31:02,037 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
   [testng] 01:31:02,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:31:02,083 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-26_01-31-02.log]
   [testng] 01:31:02,085 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration.
   [testng] [2024-04-26 01:31:02,087] [main] testng.directory = /data
   [testng] [2024-04-26 01:31:02,087] [main] testng.configDirectory = /config
   [testng] [2024-04-26 01:31:02,099] [main] testng.multiplier = 1.0
   [testng] [2024-04-26 01:31:02,099] [main] testng.in-memory = false
   [testng] [2024-04-26 01:31:02,099] [main] testng.allow-missing = false
   [testng] [2024-04-26 01:31:02,099] [main] user.language = en
   [testng] [2024-04-26 01:31:02,099] [main] user.country = ${user.country}
   [testng] [2024-04-26 01:31:02,100] [main] Maximum heap size = 13653 MB
   [testng] Scanning for files...
   [testng] [2024-04-26 01:31:02,606] [main] ----------------------------------------
   [testng] [2024-04-26 01:31:02,606] [main] Total files: 15
   [testng] [2024-04-26 01:31:02,607] [main] Scan time: 0.506 s (33 ms/file)
   [testng] [2024-04-26 01:31:02,607] [main] ----------------------------------------
   [testng] Building list of tests...
   [testng] Ready to test 14 files
   [testng] [TestNG] Running:
   [testng]   Bio-Formats software test suite
   [testng] 
   [testng] [2024-04-26 01:31:09,047] [pool-1-thread-1] Initializing /data/public/perkinelmer/PKI_fields/LuCa-7color_[13860,52919]_1x1component_data.tif: 
   [testng] 01:31:09,047 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
   [testng] 01:31:09,047 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:31:09,048 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-26_01-31-09.log]
   [testng] 01:31:09,048 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d2d7ae7 - End of configuration.
   [testng] [2024-04-26 01:31:09,127] [pool-1-thread-12] Initializing /data/perkinelmer/ROA-AB1_Scan1.qptiff: 
   [testng] 01:31:09,128 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
   [testng] 01:31:09,128 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:31:09,129 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-26_01-31-09.log]
   [testng] 01:31:09,129 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24c3fdfe - End of configuration.
   [testng] [2024-04-26 01:31:09,209] [pool-1-thread-11] Initializing /data/public/perkinelmer/PKI_scans/HandEuncompressed_Scan1.qptiff: 
   [testng] 01:31:09,209 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
   [testng] 01:31:09,209 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:31:09,210 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-26_01-31-09.log]
   [testng] 01:31:09,211 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d363cc5 - End of configuration.
   [testng] [2024-04-26 01:31:09,272] [pool-1-thread-10] Initializing /data/public/perkinelmer/PKI_fields/HandEcompressed_[11004,54205]_2x2component_data.tif: 
   [testng] 01:31:09,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
   [testng] 01:31:09,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:31:09,273 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-26_01-31-09.log]
   [testng] 01:31:09,274 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1fe3feaf - End of configuration.
   [testng] [2024-04-26 01:31:09,402] [pool-1-thread-9] Initializing /data/perkinelmer/BreastCancer7Color_Scan1.qptiff: 
   [testng] 01:31:09,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
   [testng] 01:31:09,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:31:09,404 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-26_01-31-09.log]
   [testng] 01:31:09,404 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57ae1ed9 - End of configuration.
   [testng] [2024-04-26 01:31:09,530] [pool-1-thread-8] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch8_BC2-Section16_HP_IM3_7_[19122,8127]_component_data.tif: 
   [testng] 01:31:09,531 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
   [testng] 01:31:09,531 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:31:09,532 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-26_01-31-09.log]
   [testng] 01:31:09,532 |-INFO in ch.qos.logback.core.sift.SiftProcessor@169cc1 - End of configuration.
   [testng] [2024-04-26 01:31:09,610] [pool-1-thread-7] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch6_BC2-Section6_HP_IM3_6_[13720,15451]_component_data.tif: 
   [testng] 01:31:09,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
   [testng] 01:31:09,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:31:09,612 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-26_01-31-09.log]
   [testng] 01:31:09,612 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6662694c - End of configuration.
   [testng] [2024-04-26 01:31:09,697] [pool-1-thread-6] Initializing /data/public/perkinelmer/PKI_fields/HnE_3_1x1component_data.tif: 
   [testng] 01:31:09,697 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
   [testng] 01:31:09,697 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:31:09,698 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-26_01-31-09.log]
   [testng] 01:31:09,698 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c98ed51 - End of configuration.
   [testng] [2024-04-26 01:31:09,813] [pool-1-thread-5] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch9_BC2-Section15_HP_IM3_0_[18834,16612]_component_data.tif: 
   [testng] 01:31:09,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
   [testng] 01:31:09,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:31:09,814 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-26_01-31-09.log]
   [testng] 01:31:09,815 |-INFO in ch.qos.logback.core.sift.SiftProcessor@124f61c5 - End of configuration.
   [testng] [2024-04-26 01:31:09,890] [pool-1-thread-4] Initializing /data/public/perkinelmer/PKI_scans/LuCa-7color_Scan1.qptiff: 
   [testng] 01:31:09,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
   [testng] 01:31:09,891 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:31:09,891 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-26_01-31-09.log]
   [testng] 01:31:09,892 |-INFO in ch.qos.logback.core.sift.SiftProcessor@315dfed4 - End of configuration.
   [testng] [2024-04-26 01:31:09,965] [pool-1-thread-3] Initializing /data/public/perkinelmer/PKI_scans/HandEcompressed_Scan1.qptiff: 
   [testng] 01:31:09,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
   [testng] 01:31:09,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:31:09,966 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-26_01-31-09.log]
   [testng] 01:31:09,967 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45d3f539 - End of configuration.
   [testng] [2024-04-26 01:31:10,082] [pool-1-thread-2] Initializing /data/public/perkinelmer/PKI_fields/LuCa-7color_[17572,60173]_3x3component_data.tif: 
   [testng] 01:31:10,082 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
   [testng] 01:31:10,082 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:31:10,083 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-26_01-31-10.log]
   [testng] 01:31:10,084 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5612d61e - End of configuration.
   [testng] [2024-04-26 01:31:14,861] [pool-1-thread-5] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch7_BC2-Section7_HP_IM3_0_[19914,7286]_component_data.tif: 
   [testng] [2024-04-26 01:31:14,955] [pool-1-thread-6] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch7_BC2-Section7_HP_IM3_1_[15381,15412]_component_data.tif: 
   [testng] 
   [testng] ===============================================
   [testng] Bio-Formats software test suite
   [testng] Total tests run: 742, Failures: 0, Skips: 0
   [testng] ===============================================
   [testng] 

BUILD SUCCESSFUL
Total time: 48 seconds
Finished: SUCCESS