Started by upstream project "BIOFORMATS-test-repo" build number 123
originally caused by:
Started by upstream project "Trigger" build number 140
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/jenkins3593028304056368131.sh
+ '[' vectra-qptiff = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_19211_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] 01:28:18,725 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:28:18,727 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service.
[testng] 01:28:18,727 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:28:18,728 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:28:18,728 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:28:18,728 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:28:18,728 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:28:18,728 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:28:18,729 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:28:18,729 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:28:18,730 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:28:18,730 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:28:18,884 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:28:18,884 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:28:18,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:28:18,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:28:18,910 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:28:18,910 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:28:18,910 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:28:18,910 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:28:18,910 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration.
[testng] 01:28:18,911 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point
[testng] 01:28:18,911 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 182 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-07-17 01:28:18,920] [main] java.version = 17.0.2
[testng] 01:28:18,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:28:18,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:18,961 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-17_01-28-18.log]
[testng] 01:28:18,963 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration.
[testng] [2024-07-17 01:28:18,964] [main] testng.directory = /data
[testng] [2024-07-17 01:28:18,965] [main] testng.configDirectory = /config
[testng] [2024-07-17 01:28:18,973] [main] testng.multiplier = 1.0
[testng] [2024-07-17 01:28:18,974] [main] testng.in-memory = false
[testng] [2024-07-17 01:28:18,974] [main] testng.allow-missing = false
[testng] [2024-07-17 01:28:18,974] [main] user.language = en
[testng] [2024-07-17 01:28:18,974] [main] user.country = ${user.country}
[testng] [2024-07-17 01:28:18,974] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-07-17 01:28:19,429] [main] ----------------------------------------
[testng] [2024-07-17 01:28:19,429] [main] Total files: 15
[testng] [2024-07-17 01:28:19,429] [main] Scan time: 0.455 s (30 ms/file)
[testng] [2024-07-17 01:28:19,429] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 14 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-07-17 01:28:25,324] [pool-1-thread-1] Initializing /data/public/perkinelmer/PKI_scans/LuCa-7color_Scan1.qptiff:
[testng] 01:28:25,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:28:25,325 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:25,325 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-17_01-28-25.log]
[testng] 01:28:25,326 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32070a12 - End of configuration.
[testng] [2024-07-17 01:28:25,416] [pool-1-thread-12] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch6_BC2-Section6_HP_IM3_6_[13720,15451]_component_data.tif:
[testng] 01:28:25,422 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:28:25,422 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:25,423 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-17_01-28-25.log]
[testng] 01:28:25,424 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2fd78436 - End of configuration.
[testng] [2024-07-17 01:28:25,501] [pool-1-thread-11] Initializing /data/public/perkinelmer/PKI_fields/HnE_3_1x1component_data.tif:
[testng] 01:28:25,501 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:28:25,501 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:25,502 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-17_01-28-25.log]
[testng] 01:28:25,503 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e6ea85 - End of configuration.
[testng] [2024-07-17 01:28:25,573] [pool-1-thread-10] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch7_BC2-Section7_HP_IM3_1_[15381,15412]_component_data.tif:
[testng] 01:28:25,573 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:28:25,573 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:25,574 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-17_01-28-25.log]
[testng] 01:28:25,574 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c0e4c7f - End of configuration.
[testng] [2024-07-17 01:28:25,658] [pool-1-thread-9] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch8_BC2-Section16_HP_IM3_7_[19122,8127]_component_data.tif:
[testng] 01:28:25,658 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:28:25,658 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:25,659 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-17_01-28-25.log]
[testng] 01:28:25,659 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d1e12fd - End of configuration.
[testng] [2024-07-17 01:28:25,743] [pool-1-thread-8] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch7_BC2-Section7_HP_IM3_0_[19914,7286]_component_data.tif:
[testng] 01:28:25,743 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:28:25,743 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:25,744 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-17_01-28-25.log]
[testng] 01:28:25,745 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73fa1721 - End of configuration.
[testng] [2024-07-17 01:28:25,828] [pool-1-thread-7] Initializing /data/public/perkinelmer/PKI_fields/HandEcompressed_[11004,54205]_2x2component_data.tif:
[testng] 01:28:25,828 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:28:25,828 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:25,829 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-17_01-28-25.log]
[testng] 01:28:25,830 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f26ef7 - End of configuration.
[testng] [2024-07-17 01:28:25,894] [pool-1-thread-6] Initializing /data/public/perkinelmer/PKI_fields/LuCa-7color_[13860,52919]_1x1component_data.tif:
[testng] 01:28:25,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:28:25,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:25,895 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-17_01-28-25.log]
[testng] 01:28:25,896 |-INFO in ch.qos.logback.core.sift.SiftProcessor@228aa794 - End of configuration.
[testng] [2024-07-17 01:28:25,972] [pool-1-thread-5] Initializing /data/perkinelmer/ROA-AB1_Scan1.qptiff:
[testng] 01:28:25,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:28:25,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:25,973 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-17_01-28-25.log]
[testng] 01:28:25,974 |-INFO in ch.qos.logback.core.sift.SiftProcessor@150da974 - End of configuration.
[testng] [2024-07-17 01:28:26,049] [pool-1-thread-4] Initializing /data/public/perkinelmer/PKI_scans/HandEuncompressed_Scan1.qptiff:
[testng] 01:28:26,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:28:26,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:26,050 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-17_01-28-26.log]
[testng] 01:28:26,050 |-INFO in ch.qos.logback.core.sift.SiftProcessor@123d991c - End of configuration.
[testng] [2024-07-17 01:28:26,122] [pool-1-thread-3] Initializing /data/public/perkinelmer/PKI_fields/LuCa-7color_[17572,60173]_3x3component_data.tif:
[testng] 01:28:26,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:28:26,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:26,123 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-17_01-28-26.log]
[testng] 01:28:26,123 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57869bf - End of configuration.
[testng] [2024-07-17 01:28:26,192] [pool-1-thread-2] Initializing /data/perkinelmer/BreastCancer7Color_Scan1.qptiff:
[testng] 01:28:26,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:28:26,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:26,193 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-17_01-28-26.log]
[testng] 01:28:26,193 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f8106ec - End of configuration.
[testng] [2024-07-17 01:28:29,392] [pool-1-thread-12] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch9_BC2-Section15_HP_IM3_0_[18834,16612]_component_data.tif:
[testng] [2024-07-17 01:28:29,462] [pool-1-thread-11] 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: 46 seconds
Finished: SUCCESS