Started by upstream project "BIOFORMATS-test-repo" build number 43
originally caused by:
Started by upstream project "Trigger" build number 50
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/jenkins6088789599695597075.sh
+ '[' vectra-qptiff = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_6091_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] 01:28:29,359 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:28:29,360 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service.
[testng] 01:28:29,360 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:28:29,361 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:28:29,361 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:28:29,362 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:28:29,362 |-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] 01:28:29,362 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:28:29,362 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:28:29,363 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:28:29,363 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:28:29,363 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:28:29,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:28:29,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:28:29,543 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:28:29,543 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:28:29,549 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:28:29,549 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:28:29,549 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:28:29,549 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:28:29,549 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration.
[testng] 01:28:29,550 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point
[testng] 01:28:29,550 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 188 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-04-24 01:28:29,559] [main] java.version = 17.0.2
[testng] 01:28:29,562 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:28:29,562 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:29,601 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-24_01-28-29.log]
[testng] 01:28:29,602 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration.
[testng] [2024-04-24 01:28:29,604] [main] testng.directory = /data
[testng] [2024-04-24 01:28:29,605] [main] testng.configDirectory = /config
[testng] [2024-04-24 01:28:29,613] [main] testng.multiplier = 1.0
[testng] [2024-04-24 01:28:29,613] [main] testng.in-memory = false
[testng] [2024-04-24 01:28:29,613] [main] testng.allow-missing = false
[testng] [2024-04-24 01:28:29,614] [main] user.language = en
[testng] [2024-04-24 01:28:29,614] [main] user.country = ${user.country}
[testng] [2024-04-24 01:28:29,614] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-04-24 01:28:30,079] [main] ----------------------------------------
[testng] [2024-04-24 01:28:30,080] [main] Total files: 15
[testng] [2024-04-24 01:28:30,080] [main] Scan time: 0.465 s (31 ms/file)
[testng] [2024-04-24 01:28:30,080] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 14 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-04-24 01:28:36,191] [pool-1-thread-1] Initializing /data/public/perkinelmer/PKI_scans/LuCa-7color_Scan1.qptiff:
[testng] 01:28:36,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:28:36,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:36,193 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-24_01-28-36.log]
[testng] 01:28:36,193 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3015cc1c - End of configuration.
[testng] [2024-04-24 01:28:36,288] [pool-1-thread-12] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch6_BC2-Section6_HP_IM3_6_[13720,15451]_component_data.tif:
[testng] 01:28:36,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:28:36,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:36,296 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-24_01-28-36.log]
[testng] 01:28:36,296 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f07160b - End of configuration.
[testng] [2024-04-24 01:28:36,385] [pool-1-thread-11] Initializing /data/public/perkinelmer/PKI_fields/HnE_3_1x1component_data.tif:
[testng] 01:28:36,385 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:28:36,386 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:36,387 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-24_01-28-36.log]
[testng] 01:28:36,387 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2cb19413 - End of configuration.
[testng] [2024-04-24 01:28:36,446] [pool-1-thread-10] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch7_BC2-Section7_HP_IM3_1_[15381,15412]_component_data.tif:
[testng] 01:28:36,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:28:36,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:36,447 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-24_01-28-36.log]
[testng] 01:28:36,447 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73fa1721 - End of configuration.
[testng] [2024-04-24 01:28:36,529] [pool-1-thread-9] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch8_BC2-Section16_HP_IM3_7_[19122,8127]_component_data.tif:
[testng] 01:28:36,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:28:36,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:36,530 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-24_01-28-36.log]
[testng] 01:28:36,531 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61db2856 - End of configuration.
[testng] [2024-04-24 01:28:36,618] [pool-1-thread-8] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch7_BC2-Section7_HP_IM3_0_[19914,7286]_component_data.tif:
[testng] 01:28:36,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:28:36,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:36,619 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-24_01-28-36.log]
[testng] 01:28:36,619 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f8106ec - End of configuration.
[testng] [2024-04-24 01:28:36,708] [pool-1-thread-7] Initializing /data/public/perkinelmer/PKI_fields/HandEcompressed_[11004,54205]_2x2component_data.tif:
[testng] 01:28:36,709 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:28:36,709 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:36,710 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-24_01-28-36.log]
[testng] 01:28:36,710 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4005db3c - End of configuration.
[testng] [2024-04-24 01:28:36,767] [pool-1-thread-6] Initializing /data/public/perkinelmer/PKI_fields/LuCa-7color_[13860,52919]_1x1component_data.tif:
[testng] 01:28:36,767 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:28:36,767 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:36,768 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-24_01-28-36.log]
[testng] 01:28:36,769 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d8c766f - End of configuration.
[testng] [2024-04-24 01:28:36,836] [pool-1-thread-5] Initializing /data/perkinelmer/ROA-AB1_Scan1.qptiff:
[testng] 01:28:36,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:28:36,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:36,837 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-24_01-28-36.log]
[testng] 01:28:36,838 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39fc2b8f - End of configuration.
[testng] [2024-04-24 01:28:36,936] [pool-1-thread-4] Initializing /data/public/perkinelmer/PKI_scans/HandEuncompressed_Scan1.qptiff:
[testng] 01:28:36,936 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:28:36,936 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:36,937 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-24_01-28-36.log]
[testng] 01:28:36,937 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51053046 - End of configuration.
[testng] [2024-04-24 01:28:36,997] [pool-1-thread-3] Initializing /data/public/perkinelmer/PKI_fields/LuCa-7color_[17572,60173]_3x3component_data.tif:
[testng] 01:28:36,997 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:28:36,997 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:36,998 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-24_01-28-36.log]
[testng] 01:28:36,998 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54b3bccf - End of configuration.
[testng] [2024-04-24 01:28:37,223] [pool-1-thread-2] Initializing /data/perkinelmer/BreastCancer7Color_Scan1.qptiff:
[testng] 01:28:37,224 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:28:37,224 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:37,229 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-24_01-28-37.log]
[testng] 01:28:37,252 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6193058b - End of configuration.
[testng] [2024-04-24 01:28:40,760] [pool-1-thread-12] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch9_BC2-Section15_HP_IM3_0_[18834,16612]_component_data.tif:
[testng] [2024-04-24 01:28:40,887] [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: 1 minute 5 seconds
Finished: SUCCESS