Started by upstream project "BIOFORMATS-test-repo" build number 222
originally caused by:
Started by upstream project "Trigger" build number 249
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@10
[BIOFORMATS-test-folder@10] $ /bin/bash -xe /tmp/jenkins14622047693046476916.sh
+ '[' vectra-qptiff = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_35238_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] 04:51:50,015 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 04:51:50,016 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service.
[testng] 04:51:50,016 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 04:51:50,017 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 04:51:50,017 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 04:51:50,017 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 04:51:50,018 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 04:51:50,018 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 04:51:50,018 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 04:51:50,019 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 04:51:50,019 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 04:51:50,019 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 04:51:50,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 04:51:50,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 04:51:50,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 04:51:50,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 04:51:50,195 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 04:51:50,195 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 04:51:50,195 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 04:51:50,195 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 04:51:50,196 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration.
[testng] 04:51:50,196 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point
[testng] 04:51:50,196 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 178 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-10-16 04:51:50,205] [main] java.version = 17.0.2
[testng] 04:51:50,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 04:51:50,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:51:50,245 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-16_04-51-50.log]
[testng] 04:51:50,246 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration.
[testng] [2024-10-16 04:51:50,248] [main] testng.directory = /data
[testng] [2024-10-16 04:51:50,248] [main] testng.configDirectory = /config
[testng] [2024-10-16 04:51:50,257] [main] testng.multiplier = 1.0
[testng] [2024-10-16 04:51:50,257] [main] testng.in-memory = false
[testng] [2024-10-16 04:51:50,257] [main] testng.allow-missing = false
[testng] [2024-10-16 04:51:50,257] [main] user.language = en
[testng] [2024-10-16 04:51:50,257] [main] user.country = ${user.country}
[testng] [2024-10-16 04:51:50,257] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-10-16 04:52:00,898] [main] ----------------------------------------
[testng] [2024-10-16 04:52:00,898] [main] Total files: 15
[testng] [2024-10-16 04:52:00,898] [main] Scan time: 10.64 s (709 ms/file)
[testng] [2024-10-16 04:52:00,899] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 14 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-10-16 04:54:33,070] [pool-1-thread-1] Initializing /data/public/perkinelmer/PKI_scans/HandEuncompressed_Scan1.qptiff:
[testng] 04:54:33,070 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 04:54:33,070 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:54:33,071 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-16_04-54-33.log]
[testng] 04:54:33,072 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d6ce2a2 - End of configuration.
[testng] [2024-10-16 04:54:41,915] [pool-1-thread-12] Initializing /data/public/perkinelmer/PKI_fields/HnE_3_1x1component_data.tif:
[testng] 04:54:41,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 04:54:41,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:54:41,916 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-16_04-54-41.log]
[testng] 04:54:41,916 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7519aa4a - End of configuration.
[testng] [2024-10-16 04:54:51,992] [pool-1-thread-11] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch9_BC2-Section15_HP_IM3_0_[18834,16612]_component_data.tif:
[testng] 04:54:51,992 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 04:54:51,992 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:54:51,993 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-16_04-54-51.log]
[testng] 04:54:51,993 |-INFO in ch.qos.logback.core.sift.SiftProcessor@709c66fd - End of configuration.
[testng] [2024-10-16 04:55:01,868] [pool-1-thread-10] Initializing /data/public/perkinelmer/PKI_scans/HandEcompressed_Scan1.qptiff:
[testng] 04:55:01,868 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 04:55:01,869 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:55:01,869 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-16_04-55-01.log]
[testng] 04:55:01,869 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ebac067 - End of configuration.
[testng] [2024-10-16 04:55:13,702] [pool-1-thread-9] Initializing /data/public/perkinelmer/PKI_fields/LuCa-7color_[13860,52919]_1x1component_data.tif:
[testng] 04:55:13,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 04:55:13,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:55:13,702 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-16_04-55-13.log]
[testng] 04:55:13,703 |-INFO in ch.qos.logback.core.sift.SiftProcessor@120c1530 - End of configuration.
[testng] [2024-10-16 04:55:26,166] [pool-1-thread-8] Initializing /data/public/perkinelmer/PKI_fields/HandEcompressed_[11004,54205]_2x2component_data.tif:
[testng] 04:55:26,166 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 04:55:26,166 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:55:26,167 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-16_04-55-26.log]
[testng] 04:55:26,167 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14e93d91 - End of configuration.
[testng] [2024-10-16 04:55:36,102] [pool-1-thread-7] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch7_BC2-Section7_HP_IM3_0_[19914,7286]_component_data.tif:
[testng] 04:55:36,102 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 04:55:36,103 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:55:36,103 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-16_04-55-36.log]
[testng] 04:55:36,104 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4fe9cbea - End of configuration.
[testng] [2024-10-16 04:55:47,526] [pool-1-thread-6] Initializing /data/perkinelmer/BreastCancer7Color_Scan1.qptiff:
[testng] 04:55:47,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 04:55:47,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:55:47,527 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-16_04-55-47.log]
[testng] 04:55:47,528 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e76cdec - End of configuration.
[testng] [2024-10-16 04:55:58,470] [pool-1-thread-5] Initializing /data/public/perkinelmer/PKI_fields/LuCa-7color_[17572,60173]_3x3component_data.tif:
[testng] 04:55:58,470 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 04:55:58,470 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:55:58,471 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-16_04-55-58.log]
[testng] 04:55:58,471 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ef546a7 - End of configuration.
[testng] [2024-10-16 04:56:07,696] [pool-1-thread-4] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch8_BC2-Section16_HP_IM3_7_[19122,8127]_component_data.tif:
[testng] 04:56:07,696 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 04:56:07,696 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:56:07,696 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-16_04-56-07.log]
[testng] 04:56:07,697 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d6aee4c - End of configuration.
[testng] [2024-10-16 04:56:18,416] [pool-1-thread-3] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch7_BC2-Section7_HP_IM3_1_[15381,15412]_component_data.tif:
[testng] 04:56:18,416 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 04:56:18,416 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:56:18,417 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-16_04-56-18.log]
[testng] 04:56:18,417 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52a35507 - End of configuration.
[testng] [2024-10-16 04:56:27,365] [pool-1-thread-2] Initializing /data/perkinelmer/ROA-AB1_Scan1.qptiff:
[testng] 04:56:27,365 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 04:56:27,365 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:56:27,365 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-16_04-56-27.log]
[testng] 04:56:27,366 |-INFO in ch.qos.logback.core.sift.SiftProcessor@271272da - End of configuration.
[testng] [2024-10-16 04:57:30,606] [pool-1-thread-11] Initializing /data/public/perkinelmer/PKI_scans/LuCa-7color_Scan1.qptiff:
[testng] [2024-10-16 04:57:42,369] [pool-1-thread-12] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch6_BC2-Section6_HP_IM3_6_[13720,15451]_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: 7 minutes 12 seconds
Finished: SUCCESS