Started by upstream project "BIOFORMATS-test-repo" build number 206
originally caused by:
Started by upstream project "Trigger" build number 232
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/jenkins7045207525945430788.sh
+ '[' perkinelmer-operetta = slidebook ']'
++ date +%u
+ '[' 2 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_32655_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] 01:34:54,766 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:34:54,768 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service.
[testng] 01:34:54,768 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:34:54,769 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:34:54,770 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:34:54,770 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:34:54,771 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:34:54,771 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:34:54,771 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:34:54,772 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:34:54,773 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:34:54,773 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:34:54,967 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:34:54,967 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:34:54,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:34:54,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:34:55,001 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:34:55,001 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:34:55,001 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:34:55,002 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:34:55,002 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration.
[testng] 01:34:55,003 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point
[testng] 01:34:55,003 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 232 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-10-01 01:34:55,014] [main] java.version = 11.0.16
[testng] 01:34:55,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:34:55,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:34:55,083 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-01_01-34-55.log]
[testng] 01:34:55,085 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
[testng] [2024-10-01 01:34:55,087] [main] testng.directory = /data
[testng] [2024-10-01 01:34:55,087] [main] testng.configDirectory = /config
[testng] [2024-10-01 01:34:55,098] [main] testng.multiplier = 1.0
[testng] [2024-10-01 01:34:55,099] [main] testng.in-memory = false
[testng] [2024-10-01 01:34:55,100] [main] testng.allow-missing = false
[testng] [2024-10-01 01:34:55,100] [main] user.language = en
[testng] [2024-10-01 01:34:55,100] [main] user.country = ${user.country}
[testng] [2024-10-01 01:34:55,100] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-10-01 01:38:19,761] [main] ----------------------------------------
[testng] [2024-10-01 01:38:19,762] [main] Total files: 14663
[testng] [2024-10-01 01:38:19,762] [main] Scan time: 204.661 s (13 ms/file)
[testng] [2024-10-01 01:38:19,762] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 16 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-10-01 01:40:04,175] [pool-1-thread-1] Initializing /data/public/idr0034/HipSci Experiment 10 Plate 1__2014-08-21T17_57_35-Measurement1/Images/Index.idx.xml:
[testng] 01:40:04,176 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:40:04,176 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:40:04,178 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-01_01-40-04.log]
[testng] 01:40:04,178 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b2f38f8 - End of configuration.
[testng] [2024-10-01 01:40:04,973] [pool-1-thread-12] Initializing /data/samples/no-first-series/Index.idx.xml:
[testng] 01:40:04,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:40:04,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:40:04,974 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-01_01-40-04.log]
[testng] 01:40:04,975 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e8131 - End of configuration.
[testng] [2024-10-01 01:40:05,018] [pool-1-thread-11] Initializing /data/public/omer/006P_M3/006P_M3_overview_fields.png:
[testng] 01:40:05,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:40:05,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:40:05,019 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-01_01-40-05.log]
[testng] 01:40:05,020 |-INFO in ch.qos.logback.core.sift.SiftProcessor@169da846 - End of configuration.
[testng] [2024-10-01 01:40:05,029] [pool-1-thread-10] Initializing /data/stephen/P004-CC Edu-pHH3__2009-02-03T17_36_29-Measurement1/Images/Index.idx.xml:
[testng] 01:40:05,029 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:40:05,029 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:40:05,030 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-01_01-40-05.log]
[testng] 01:40:05,030 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f278d82 - End of configuration.
[testng] [2024-10-01 01:40:05,092] [pool-1-thread-9] Initializing /data/hms/ryang_skbr3_p1__2012-07-10T15_24_30-Measurement1/Images/Index.idx.xml:
[testng] 01:40:05,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:40:05,093 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:40:05,093 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-01_01-40-05.log]
[testng] 01:40:05,094 |-INFO in ch.qos.logback.core.sift.SiftProcessor@494354bb - End of configuration.
[testng] [2024-10-01 01:40:05,142] [pool-1-thread-8] Initializing /data/samples/new-phenix/artificial-v6/Hiplex_run1_cycle1_MsPos/Index.idx.xml:
[testng] 01:40:05,142 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:40:05,142 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:40:05,143 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-01_01-40-05.log]
[testng] 01:40:05,143 |-INFO in ch.qos.logback.core.sift.SiftProcessor@269731dc - End of configuration.
[testng] [2024-10-01 01:40:05,454] [pool-1-thread-7] Initializing /data/pki/Export/HRMNY-13786__2021-11-23T13_44_30-Measurement 3/Images/Index.xml:
[testng] 01:40:05,454 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:40:05,454 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:40:05,455 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-01_01-40-05.log]
[testng] 01:40:05,456 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15287935 - End of configuration.
[testng] [2024-10-01 01:40:05,600] [pool-1-thread-6] Initializing /data/public/zenodo-7841360/Hoechst__2023-03-07T10_17_54-Measurement 2/Images/Index.idx.xml:
[testng] 01:40:05,600 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:40:05,600 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:40:05,601 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-01_01-40-05.log]
[testng] 01:40:05,602 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55152925 - End of configuration.
[testng] [2024-10-01 01:40:05,632] [pool-1-thread-5] Initializing /data/public/omer/006P_M3/006P__2017-08-19T12_42_59-Measurement 3/Images/Index.idx.xml:
[testng] 01:40:05,632 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:40:05,632 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:40:05,633 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-01_01-40-05.log]
[testng] 01:40:05,634 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76d0b25f - End of configuration.
[testng] [2024-10-01 01:40:05,931] [pool-1-thread-4] Initializing /data/qa-17826/JLM-20170801-Operetta/Index.idx.xml:
[testng] 01:40:05,932 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:40:05,932 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:40:05,933 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-01_01-40-05.log]
[testng] 01:40:05,933 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ae7df94 - End of configuration.
[testng] [2024-10-01 01:40:05,981] [pool-1-thread-3] Initializing /data/stephen/Plate 1(2)__2011-09-29T23_50_20-Measurement1/Images/Index.idx.xml:
[testng] 01:40:05,982 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:40:05,982 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:40:05,982 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-01_01-40-05.log]
[testng] 01:40:05,983 |-INFO in ch.qos.logback.core.sift.SiftProcessor@273f6dc7 - End of configuration.
[testng] [2024-10-01 01:40:06,046] [pool-1-thread-2] Initializing /data/samples/32-bit-file/Index.idx.xml:
[testng] 01:40:06,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:40:06,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:40:06,047 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-01_01-40-06.log]
[testng] 01:40:06,047 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7753c493 - End of configuration.
[testng] [2024-10-01 01:40:07,417] [pool-1-thread-11] Initializing /data/samples/smaller-xy/Index.idx.xml:
[testng] [2024-10-01 01:40:08,032] [pool-1-thread-6] Initializing /data/public/omer/006P_M3/006P_M3_overview.png:
[testng] [2024-10-01 01:40:08,955] [pool-1-thread-6] Initializing /data/pki/DataSet/dec61bf8-5ca8-415a-8639-b75bf59ca47c/images/index.xml:
[testng] [2024-10-01 01:40:18,233] [pool-1-thread-9] Initializing /data/samples/new-phenix/original/Hiplex_run1_cycle1_MsPos/Index.idx.xml:
[testng] 03:01:09,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 03:01:09,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:01:09,140 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-01_03-01-09.log]
[testng] 03:01:09,141 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dd09650 - End of configuration.
[testng] 03:01:38,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 03:01:38,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:01:38,092 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-01_03-01-38.log]
[testng] 03:01:38,092 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71238d31 - End of configuration.
[testng] 03:02:09,215 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 03:02:09,215 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:02:09,216 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-01_03-02-09.log]
[testng] 03:02:09,217 |-INFO in ch.qos.logback.core.sift.SiftProcessor@465c7258 - End of configuration.
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 848, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 87 minutes 18 seconds
Finished: SUCCESS