Started by upstream project "BIOFORMATS-test-repo" build number 93
originally caused by:
Started by upstream project "Trigger" build number 104
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2
[BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins7101006141267950415.sh
+ '[' vectra-qptiff = slidebook ']'
++ date +%u
+ '[' 6 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_14291_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] WARNING: An illegal reflective access operation has occurred
[testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket
[testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener
[testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
[testng] WARNING: All illegal access operations will be denied in a future release
[testng] File leak detector installed
[testng] 01:29:17,510 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:29:17,515 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service.
[testng] 01:29:17,515 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:29:17,519 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:29:17,521 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:29:17,522 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:29:17,524 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 5 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:29:17,524 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:29:17,526 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:29:17,529 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:29:17,529 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:29:17,530 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:29:17,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:29:17,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:29:17,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:29:17,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:29:17,885 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:29:17,885 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:29:17,885 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:29:17,886 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:29:17,886 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration.
[testng] 01:29:17,887 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point
[testng] 01:29:17,887 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 361 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-06-15 01:29:17,900] [main] java.version = 11.0.16
[testng] 01:29:17,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:29:17,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:29:17,975 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-15_01-29-17.log]
[testng] 01:29:17,977 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
[testng] [2024-06-15 01:29:17,980] [main] testng.directory = /data
[testng] [2024-06-15 01:29:17,980] [main] testng.configDirectory = /config
[testng] [2024-06-15 01:29:17,997] [main] testng.multiplier = 1.0
[testng] [2024-06-15 01:29:18,000] [main] testng.in-memory = false
[testng] [2024-06-15 01:29:18,000] [main] testng.allow-missing = false
[testng] [2024-06-15 01:29:18,000] [main] user.language = en
[testng] [2024-06-15 01:29:18,000] [main] user.country = ${user.country}
[testng] [2024-06-15 01:29:18,000] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-06-15 01:29:18,720] [main] ----------------------------------------
[testng] [2024-06-15 01:29:18,720] [main] Total files: 15
[testng] [2024-06-15 01:29:18,720] [main] Scan time: 0.718 s (47 ms/file)
[testng] [2024-06-15 01:29:18,720] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 14 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-06-15 01:29:25,916] [pool-1-thread-1] Initializing /data/public/perkinelmer/PKI_fields/LuCa-7color_[17572,60173]_3x3component_data.tif:
[testng] 01:29:25,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:29:25,919 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:29:25,923 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-15_01-29-25.log]
[testng] 01:29:25,924 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45baa85d - End of configuration.
[testng] [2024-06-15 01:29:26,110] [pool-1-thread-12] Initializing /data/public/perkinelmer/PKI_fields/HnE_3_1x1component_data.tif:
[testng] 01:29:26,111 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:29:26,111 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:29:26,140 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-15_01-29-26.log]
[testng] 01:29:26,141 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68b54c21 - End of configuration.
[testng] [2024-06-15 01:29:26,249] [pool-1-thread-11] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch7_BC2-Section7_HP_IM3_0_[19914,7286]_component_data.tif:
[testng] 01:29:26,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:29:26,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:29:26,251 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-15_01-29-26.log]
[testng] 01:29:26,251 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ee5b0c7 - End of configuration.
[testng] [2024-06-15 01:29:26,416] [pool-1-thread-10] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch6_BC2-Section6_HP_IM3_6_[13720,15451]_component_data.tif:
[testng] 01:29:26,416 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:29:26,416 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:29:26,417 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-15_01-29-26.log]
[testng] 01:29:26,418 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78ee61ab - End of configuration.
[testng] [2024-06-15 01:29:26,532] [pool-1-thread-9] Initializing /data/public/perkinelmer/PKI_scans/LuCa-7color_Scan1.qptiff:
[testng] 01:29:26,532 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:29:26,532 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:29:26,533 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-15_01-29-26.log]
[testng] 01:29:26,534 |-INFO in ch.qos.logback.core.sift.SiftProcessor@16ed5be4 - End of configuration.
[testng] [2024-06-15 01:29:26,641] [pool-1-thread-8] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch7_BC2-Section7_HP_IM3_1_[15381,15412]_component_data.tif:
[testng] 01:29:26,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:29:26,642 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:29:26,643 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-15_01-29-26.log]
[testng] 01:29:26,643 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4db84aa6 - End of configuration.
[testng] [2024-06-15 01:29:26,734] [pool-1-thread-7] Initializing /data/public/perkinelmer/PKI_scans/HandEcompressed_Scan1.qptiff:
[testng] 01:29:26,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:29:26,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:29:26,735 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-15_01-29-26.log]
[testng] 01:29:26,736 |-INFO in ch.qos.logback.core.sift.SiftProcessor@625d44db - End of configuration.
[testng] [2024-06-15 01:29:26,825] [pool-1-thread-6] Initializing /data/perkinelmer/BreastCancer7Color_Scan1.qptiff:
[testng] 01:29:26,826 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:29:26,826 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:29:26,827 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-15_01-29-26.log]
[testng] 01:29:26,827 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f886058 - End of configuration.
[testng] [2024-06-15 01:29:26,961] [pool-1-thread-5] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch8_BC2-Section16_HP_IM3_7_[19122,8127]_component_data.tif:
[testng] 01:29:26,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:29:26,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:29:26,963 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-15_01-29-26.log]
[testng] 01:29:26,964 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7914afa9 - End of configuration.
[testng] [2024-06-15 01:29:27,110] [pool-1-thread-4] Initializing /data/public/perkinelmer/PKI_fields/LuCa-7color_[13860,52919]_1x1component_data.tif:
[testng] 01:29:27,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:29:27,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:29:27,111 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-15_01-29-27.log]
[testng] 01:29:27,111 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38de452b - End of configuration.
[testng] [2024-06-15 01:29:27,187] [pool-1-thread-3] Initializing /data/public/perkinelmer/PKI_fields/HandEcompressed_[11004,54205]_2x2component_data.tif:
[testng] 01:29:27,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:29:27,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:29:27,188 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-15_01-29-27.log]
[testng] 01:29:27,189 |-INFO in ch.qos.logback.core.sift.SiftProcessor@189bf79d - End of configuration.
[testng] [2024-06-15 01:29:27,279] [pool-1-thread-2] Initializing /data/perkinelmer/ROA-AB1_Scan1.qptiff:
[testng] 01:29:27,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:29:27,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:29:27,281 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-15_01-29-27.log]
[testng] 01:29:27,282 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12e898bc - End of configuration.
[testng] [2024-06-15 01:29:32,384] [pool-1-thread-5] Initializing /data/public/perkinelmer/PKI_scans/HandEuncompressed_Scan1.qptiff:
[testng] [2024-06-15 01:29:32,467] [pool-1-thread-11] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch9_BC2-Section15_HP_IM3_0_[18834,16612]_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: 1 minute 7 seconds
Finished: SUCCESS