Skip to content
[Jenkins]Jenkins
log in

Console Output

Started by upstream project "BIOFORMATS-test-repo" build number 101
originally caused by:
 Started by upstream project "Trigger" build number 112
 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/jenkins4371312377595554255.sh
+ '[' vectra-qptiff = slidebook ']'
++ date +%u
+ '[' 7 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_15603_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
    [javac] warning: [options] bootstrap class path not set in conjunction with -source 8
    [javac] 1 warning

test-automated:
   [testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket
   [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket
   [testng] File leak detector installed
   [testng] 01:28:35,541 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
   [testng] 01:28:35,542 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service.
   [testng] 01:28:35,542 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 01:28:35,543 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 01:28:35,543 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
   [testng] 01:28:35,544 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
   [testng] 01:28:35,544 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
   [testng] 01:28:35,544 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 01:28:35,544 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 01:28:35,545 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
   [testng] 01:28:35,545 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
   [testng] 01:28:35,545 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
   [testng] 01:28:35,706 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
   [testng] 01:28:35,706 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
   [testng] 01:28:35,728 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
   [testng] 01:28:35,728 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
   [testng] 01:28:35,734 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
   [testng] 01:28:35,734 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
   [testng] 01:28:35,734 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
   [testng] 01:28:35,735 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
   [testng] 01:28:35,735 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration.
   [testng] 01:28:35,736 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point
   [testng] 01:28:35,736 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 192 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
   [testng] [2024-06-23 01:28:35,745] [main] java.version = 17.0.2
   [testng] 01:28:35,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
   [testng] 01:28:35,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:28:35,788 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-23_01-28-35.log]
   [testng] 01:28:35,789 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration.
   [testng] [2024-06-23 01:28:35,791] [main] testng.directory = /data
   [testng] [2024-06-23 01:28:35,792] [main] testng.configDirectory = /config
   [testng] [2024-06-23 01:28:35,800] [main] testng.multiplier = 1.0
   [testng] [2024-06-23 01:28:35,801] [main] testng.in-memory = false
   [testng] [2024-06-23 01:28:35,801] [main] testng.allow-missing = false
   [testng] [2024-06-23 01:28:35,801] [main] user.language = en
   [testng] [2024-06-23 01:28:35,801] [main] user.country = ${user.country}
   [testng] [2024-06-23 01:28:35,801] [main] Maximum heap size = 15360 MB
   [testng] Scanning for files...
   [testng] [2024-06-23 01:28:36,196] [main] ----------------------------------------
   [testng] [2024-06-23 01:28:36,197] [main] Total files: 15
   [testng] [2024-06-23 01:28:36,197] [main] Scan time: 0.395 s (26 ms/file)
   [testng] [2024-06-23 01:28:36,197] [main] ----------------------------------------
   [testng] Building list of tests...
   [testng] Ready to test 14 files
   [testng] [TestNG] Running:
   [testng]   Bio-Formats software test suite
   [testng] 
   [testng] [2024-06-23 01:28:42,227] [pool-1-thread-1] Initializing /data/public/perkinelmer/PKI_scans/LuCa-7color_Scan1.qptiff: 
   [testng] 01:28:42,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
   [testng] 01:28:42,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:28:42,229 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-23_01-28-42.log]
   [testng] 01:28:42,229 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e3cd643 - End of configuration.
   [testng] [2024-06-23 01:28:42,323] [pool-1-thread-12] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch6_BC2-Section6_HP_IM3_6_[13720,15451]_component_data.tif: 
   [testng] 01:28:42,331 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
   [testng] 01:28:42,331 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:28:42,332 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-23_01-28-42.log]
   [testng] 01:28:42,332 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31da32d2 - End of configuration.
   [testng] [2024-06-23 01:28:42,427] [pool-1-thread-11] Initializing /data/public/perkinelmer/PKI_fields/HnE_3_1x1component_data.tif: 
   [testng] 01:28:42,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
   [testng] 01:28:42,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:28:42,428 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-23_01-28-42.log]
   [testng] 01:28:42,428 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31dab9a0 - End of configuration.
   [testng] [2024-06-23 01:28:42,504] [pool-1-thread-10] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch7_BC2-Section7_HP_IM3_1_[15381,15412]_component_data.tif: 
   [testng] 01:28:42,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
   [testng] 01:28:42,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:28:42,506 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-23_01-28-42.log]
   [testng] 01:28:42,506 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f26ef7 - End of configuration.
   [testng] [2024-06-23 01:28:42,605] [pool-1-thread-9] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch8_BC2-Section16_HP_IM3_7_[19122,8127]_component_data.tif: 
   [testng] 01:28:42,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
   [testng] 01:28:42,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:28:42,607 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-23_01-28-42.log]
   [testng] 01:28:42,607 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60dedb26 - End of configuration.
   [testng] [2024-06-23 01:28:42,704] [pool-1-thread-8] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch7_BC2-Section7_HP_IM3_0_[19914,7286]_component_data.tif: 
   [testng] 01:28:42,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
   [testng] 01:28:42,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:28:42,705 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-23_01-28-42.log]
   [testng] 01:28:42,705 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4005db3c - End of configuration.
   [testng] [2024-06-23 01:28:42,790] [pool-1-thread-7] Initializing /data/public/perkinelmer/PKI_fields/HandEcompressed_[11004,54205]_2x2component_data.tif: 
   [testng] 01:28:42,790 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
   [testng] 01:28:42,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:28:42,791 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-23_01-28-42.log]
   [testng] 01:28:42,792 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d8c766f - End of configuration.
   [testng] [2024-06-23 01:28:42,859] [pool-1-thread-6] Initializing /data/public/perkinelmer/PKI_fields/LuCa-7color_[13860,52919]_1x1component_data.tif: 
   [testng] 01:28:42,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
   [testng] 01:28:42,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:28:42,860 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-23_01-28-42.log]
   [testng] 01:28:42,861 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54b3bccf - End of configuration.
   [testng] [2024-06-23 01:28:42,951] [pool-1-thread-5] Initializing /data/perkinelmer/ROA-AB1_Scan1.qptiff: 
   [testng] 01:28:42,951 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
   [testng] 01:28:42,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:28:42,952 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-23_01-28-42.log]
   [testng] 01:28:42,953 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6193058b - End of configuration.
   [testng] [2024-06-23 01:28:43,036] [pool-1-thread-4] Initializing /data/public/perkinelmer/PKI_scans/HandEuncompressed_Scan1.qptiff: 
   [testng] 01:28:43,036 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
   [testng] 01:28:43,037 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:28:43,037 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-23_01-28-43.log]
   [testng] 01:28:43,037 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e36f230 - End of configuration.
   [testng] [2024-06-23 01:28:43,098] [pool-1-thread-3] Initializing /data/public/perkinelmer/PKI_fields/LuCa-7color_[17572,60173]_3x3component_data.tif: 
   [testng] 01:28:43,098 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
   [testng] 01:28:43,098 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:28:43,099 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-23_01-28-43.log]
   [testng] 01:28:43,100 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18a4f4bd - End of configuration.
   [testng] [2024-06-23 01:28:43,164] [pool-1-thread-2] Initializing /data/perkinelmer/BreastCancer7Color_Scan1.qptiff: 
   [testng] 01:28:43,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
   [testng] 01:28:43,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 01:28:43,165 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-23_01-28-43.log]
   [testng] 01:28:43,165 |-INFO in ch.qos.logback.core.sift.SiftProcessor@694de05f - End of configuration.
   [testng] [2024-06-23 01:28:46,837] [pool-1-thread-8] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch9_BC2-Section15_HP_IM3_0_[18834,16612]_component_data.tif: 
   [testng] [2024-06-23 01:28:46,934] [pool-1-thread-10] Initializing /data/public/perkinelmer/PKI_scans/HandEcompressed_Scan1.qptiff: 
   [testng] 
   [testng] ===============================================
   [testng] Bio-Formats software test suite
   [testng] Total tests run: 742, Failures: 0, Skips: 0
   [testng] ===============================================
   [testng] 

BUILD SUCCESSFUL
Total time: 50 seconds
Finished: SUCCESS