Started by upstream project "BIOFORMATS-test-repo" build number 81
originally caused by:
Started by upstream project "Trigger" build number 89
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9
[BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins16445752963286057202.sh
+ '[' perkinelmer-operetta = slidebook ']'
++ date +%u
+ '[' 6 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_12312_merge_ci -v /uod/idr/repos/curated/perkinelmer-operetta:/data -v /uod/idr-scratch/merge-ci/curated/perkinelmer-operetta:/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] 01:28:23,763 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:28:23,765 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service.
[testng] 01:28:23,765 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:28:23,766 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:28:23,767 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:28:23,767 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:28:23,767 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:28:23,767 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:28:23,768 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:28:23,769 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:28:23,769 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:28:23,769 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:28:23,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:28:23,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:28:23,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:28:23,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:28:23,968 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:28:23,968 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:28:23,968 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:28:23,969 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:28:23,969 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration.
[testng] 01:28:23,970 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point
[testng] 01:28:23,970 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 202 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-06-01 01:28:23,979] [main] java.version = 11.0.16
[testng] 01:28:23,982 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:28:23,982 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:28:24,024 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-01_01-28-23.log]
[testng] 01:28:24,026 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
[testng] [2024-06-01 01:28:24,028] [main] testng.directory = /data
[testng] [2024-06-01 01:28:24,029] [main] testng.configDirectory = /config
[testng] [2024-06-01 01:28:24,038] [main] testng.multiplier = 1.0
[testng] [2024-06-01 01:28:24,040] [main] testng.in-memory = false
[testng] [2024-06-01 01:28:24,040] [main] testng.allow-missing = false
[testng] [2024-06-01 01:28:24,040] [main] user.language = en
[testng] [2024-06-01 01:28:24,040] [main] user.country = ${user.country}
[testng] [2024-06-01 01:28:24,040] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-06-01 01:29:20,276] [main] ----------------------------------------
[testng] [2024-06-01 01:29:20,277] [main] Total files: 14659
[testng] [2024-06-01 01:29:20,277] [main] Scan time: 56.236 s (3 ms/file)
[testng] [2024-06-01 01:29:20,277] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 15 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-06-01 01:30:06,936] [pool-1-thread-1] Initializing /data/pki/Export/HRMNY-13786__2021-11-23T13_44_30-Measurement 3/Images/Index.xml:
[testng] 01:30:06,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:30:06,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:30:06,939 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-01_01-30-06.log]
[testng] 01:30:06,940 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6086d88 - End of configuration.
[testng] [2024-06-01 01:30:07,033] [pool-1-thread-12] Initializing /data/public/omer/006P_M3/006P_M3_overview_fields.png:
[testng] 01:30:07,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:30:07,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:30:07,034 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-01_01-30-07.log]
[testng] 01:30:07,034 |-INFO in ch.qos.logback.core.sift.SiftProcessor@378272c5 - End of configuration.
[testng] [2024-06-01 01:30:07,043] [pool-1-thread-11] Initializing /data/samples/new-phenix/original/Hiplex_run1_cycle1_MsPos/Index.idx.xml:
[testng] 01:30:07,043 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:30:07,043 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:30:07,044 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-01_01-30-07.log]
[testng] 01:30:07,045 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5879f041 - End of configuration.
[testng] [2024-06-01 01:30:07,597] [pool-1-thread-10] Initializing /data/public/omer/006P_M3/006P_M3_overview.png:
[testng] 01:30:07,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:30:07,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:30:07,598 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-01_01-30-07.log]
[testng] 01:30:07,598 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2921118b - End of configuration.
[testng] [2024-06-01 01:30:07,606] [pool-1-thread-9] Initializing /data/public/idr0034/HipSci Experiment 10 Plate 1__2014-08-21T17_57_35-Measurement1/Images/Index.idx.xml:
[testng] 01:30:07,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:30:07,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:30:07,607 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-01_01-30-07.log]
[testng] 01:30:07,607 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1001100 - End of configuration.
[testng] [2024-06-01 01:30:08,535] [pool-1-thread-8] Initializing /data/samples/no-first-series/Index.idx.xml:
[testng] 01:30:08,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:30:08,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:30:08,536 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-01_01-30-08.log]
[testng] 01:30:08,536 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6447013d - End of configuration.
[testng] [2024-06-01 01:30:08,554] [pool-1-thread-7] Initializing /data/samples/smaller-xy/Index.idx.xml:
[testng] 01:30:08,555 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:30:08,555 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:30:08,555 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-01_01-30-08.log]
[testng] 01:30:08,556 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f5fa55d - End of configuration.
[testng] [2024-06-01 01:30:08,577] [pool-1-thread-6] Initializing /data/qa-17826/JLM-20170801-Operetta/Index.idx.xml:
[testng] 01:30:08,577 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:30:08,577 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:30:08,577 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-01_01-30-08.log]
[testng] 01:30:08,578 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2abee1a5 - End of configuration.
[testng] [2024-06-01 01:30:08,611] [pool-1-thread-5] Initializing /data/public/omer/006P_M3/006P__2017-08-19T12_42_59-Measurement 3/Images/Index.idx.xml:
[testng] 01:30:08,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:30:08,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:30:08,612 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-01_01-30-08.log]
[testng] 01:30:08,613 |-INFO in ch.qos.logback.core.sift.SiftProcessor@132634d6 - End of configuration.
[testng] [2024-06-01 01:30:08,833] [pool-1-thread-4] Initializing /data/pki/DataSet/dec61bf8-5ca8-415a-8639-b75bf59ca47c/images/index.xml:
[testng] 01:30:08,834 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:30:08,834 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:30:08,834 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-01_01-30-08.log]
[testng] 01:30:08,835 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43ebf7a9 - End of configuration.
[testng] [2024-06-01 01:30:08,864] [pool-1-thread-3] Initializing /data/stephen/P004-CC Edu-pHH3__2009-02-03T17_36_29-Measurement1/Images/Index.idx.xml:
[testng] 01:30:08,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:30:08,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:30:08,865 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-01_01-30-08.log]
[testng] 01:30:08,865 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25dde47d - End of configuration.
[testng] [2024-06-01 01:30:08,898] [pool-1-thread-2] Initializing /data/samples/32-bit-file/Index.idx.xml:
[testng] 01:30:08,898 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:30:08,899 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:30:08,899 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-01_01-30-08.log]
[testng] 01:30:08,899 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49884958 - End of configuration.
[testng] [2024-06-01 01:30:10,358] [pool-1-thread-10] Initializing /data/hms/ryang_skbr3_p1__2012-07-10T15_24_30-Measurement1/Images/Index.idx.xml:
[testng] [2024-06-01 01:30:10,386] [pool-1-thread-12] Initializing /data/samples/new-phenix/artificial-v6/Hiplex_run1_cycle1_MsPos/Index.idx.xml:
[testng] [2024-06-01 01:30:18,135] [pool-1-thread-8] Initializing /data/stephen/Plate 1(2)__2011-09-29T23_50_20-Measurement1/Images/Index.idx.xml:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 795, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 16 minutes 42 seconds
Finished: SUCCESS