Started by upstream project "BIOFORMATS-test-repo" build number 299
originally caused by:
Started by upstream project "Trigger" build number 321
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/jenkins9076191573086837467.sh
+ '[' perkinelmer-operetta = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_47272_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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release
[javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
[javac] 4 warnings
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] 00:45:35,343 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 00:45:35,344 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service.
[testng] 00:45:35,344 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:45:35,345 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:45:35,345 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 00:45:35,346 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 00:45:35,346 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 00:45:35,346 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:45:35,346 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:45:35,347 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 00:45:35,347 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 00:45:35,347 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 00:45:35,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 00:45:35,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 00:45:35,529 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 00:45:35,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 00:45:35,536 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 00:45:35,536 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 00:45:35,536 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 00:45:35,536 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 00:45:35,536 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration.
[testng] 00:45:35,537 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point
[testng] 00:45:35,537 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 191 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-12-26 00:45:35,546] [main] java.version = 21
[testng] 00:45:35,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 00:45:35,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:45:35,590 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-26_00-45-35.log]
[testng] 00:45:35,592 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration.
[testng] [2024-12-26 00:45:35,593] [main] testng.directory = /data
[testng] [2024-12-26 00:45:35,594] [main] testng.configDirectory = /config
[testng] [2024-12-26 00:45:35,607] [main] testng.multiplier = 1.0
[testng] [2024-12-26 00:45:35,608] [main] testng.in-memory = false
[testng] [2024-12-26 00:45:35,608] [main] testng.allow-missing = false
[testng] [2024-12-26 00:45:35,608] [main] user.language = en
[testng] [2024-12-26 00:45:35,608] [main] user.country = ${user.country}
[testng] [2024-12-26 00:45:35,608] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-12-26 00:57:27,013] [main] ----------------------------------------
[testng] [2024-12-26 00:57:27,013] [main] Total files: 14681
[testng] [2024-12-26 00:57:27,013] [main] Scan time: 711.405 s (48 ms/file)
[testng] [2024-12-26 00:57:27,014] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 17 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-12-26 01:09:35,529] [pool-1-thread-1] Initializing /data/public/omer/006P_M3/006P_M3_overview_fields.png:
[testng] 01:09:35,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:09:35,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:09:35,531 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-26_01-09-35.log]
[testng] 01:09:35,532 |-INFO in ch.qos.logback.core.sift.SiftProcessor@556849a8 - End of configuration.
[testng] [2024-12-26 01:09:35,608] [pool-1-thread-12] Initializing /data/samples/extra-directories/Index.idx.xml:
[testng] 01:09:35,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:09:35,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:09:35,609 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-26_01-09-35.log]
[testng] 01:09:35,609 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d9b8a9 - End of configuration.
[testng] [2024-12-26 01:09:36,774] [pool-1-thread-11] Initializing /data/pki/DataSet/dec61bf8-5ca8-415a-8639-b75bf59ca47c/images/index.xml:
[testng] 01:09:36,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:09:36,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:09:36,776 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-26_01-09-36.log]
[testng] 01:09:36,777 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2dffef26 - End of configuration.
[testng] [2024-12-26 01:09:38,323] [pool-1-thread-10] Initializing /data/stephen/P004-CC Edu-pHH3__2009-02-03T17_36_29-Measurement1/Images/Index.idx.xml:
[testng] 01:09:38,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:09:38,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:09:38,325 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-26_01-09-38.log]
[testng] 01:09:38,325 |-INFO in ch.qos.logback.core.sift.SiftProcessor@606d36f1 - End of configuration.
[testng] [2024-12-26 01:09:39,862] [pool-1-thread-9] Initializing /data/samples/smaller-xy/Index.idx.xml:
[testng] 01:09:39,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:09:39,863 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:09:39,863 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-26_01-09-39.log]
[testng] 01:09:39,864 |-INFO in ch.qos.logback.core.sift.SiftProcessor@349d1354 - End of configuration.
[testng] [2024-12-26 01:09:41,406] [pool-1-thread-8] Initializing /data/qa-17826/JLM-20170801-Operetta/Index.idx.xml:
[testng] 01:09:41,406 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:09:41,406 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:09:41,407 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-26_01-09-41.log]
[testng] 01:09:41,407 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54bc5e7e - End of configuration.
[testng] [2024-12-26 01:09:47,077] [pool-1-thread-7] Initializing /data/public/idr0034/HipSci Experiment 10 Plate 1__2014-08-21T17_57_35-Measurement1/Images/Index.idx.xml:
[testng] 01:09:47,077 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:09:47,077 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:09:47,078 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-26_01-09-47.log]
[testng] 01:09:47,078 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5bf2783e - End of configuration.
[testng] [2024-12-26 01:10:17,184] [pool-1-thread-6] Initializing /data/samples/32-bit-file/Index.idx.xml:
[testng] 01:10:17,184 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:10:17,185 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:10:17,185 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-26_01-10-17.log]
[testng] 01:10:17,186 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bd13bee - End of configuration.
[testng] [2024-12-26 01:10:18,009] [pool-1-thread-5] Initializing /data/pki/Export/HRMNY-13786__2021-11-23T13_44_30-Measurement 3/Images/Index.xml:
[testng] 01:10:18,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:10:18,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:10:18,010 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-26_01-10-18.log]
[testng] 01:10:18,010 |-INFO in ch.qos.logback.core.sift.SiftProcessor@207ca128 - End of configuration.
[testng] [2024-12-26 01:10:19,562] [pool-1-thread-4] Initializing /data/stephen/Plate 1(2)__2011-09-29T23_50_20-Measurement1/Images/Index.idx.xml:
[testng] 01:10:19,562 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:10:19,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:10:19,563 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-26_01-10-19.log]
[testng] 01:10:19,563 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54047901 - End of configuration.
[testng] [2024-12-26 01:10:20,482] [pool-1-thread-3] Initializing /data/samples/no-first-series/Index.idx.xml:
[testng] 01:10:20,482 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:10:20,482 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:10:20,483 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-26_01-10-20.log]
[testng] 01:10:20,483 |-INFO in ch.qos.logback.core.sift.SiftProcessor@310e1db0 - End of configuration.
[testng] [2024-12-26 01:10:21,543] [pool-1-thread-2] Initializing /data/samples/new-phenix/original/Hiplex_run1_cycle1_MsPos/Index.idx.xml:
[testng] 01:10:21,543 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:10:21,543 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:10:21,543 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-26_01-10-21.log]
[testng] 01:10:21,544 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d45bdeb - End of configuration.
[testng] [2024-12-26 01:10:34,858] [pool-1-thread-1] Initializing /data/public/zenodo-7841360/Hoechst__2023-03-07T10_17_54-Measurement 2/Images/Index.idx.xml:
[testng] [2024-12-26 01:10:49,951] [pool-1-thread-1] Initializing /data/public/omer/006P_M3/006P__2017-08-19T12_42_59-Measurement 3/Images/Index.idx.xml:
[testng] [2024-12-26 01:11:35,981] [pool-1-thread-3] Initializing /data/hms/ryang_skbr3_p1__2012-07-10T15_24_30-Measurement1/Images/Index.idx.xml:
[testng] [2024-12-26 01:11:40,844] [pool-1-thread-8] Initializing /data/public/omer/006P_M3/006P_M3_overview.png:
[testng] [2024-12-26 01:11:42,996] [pool-1-thread-9] Initializing /data/samples/new-phenix/artificial-v6/Hiplex_run1_cycle1_MsPos/Index.idx.xml:
[testng] 03:46:08,717 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 03:46:08,717 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:46:08,718 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-26_03-46-08.log]
[testng] 03:46:08,718 |-INFO in ch.qos.logback.core.sift.SiftProcessor@238bfc56 - End of configuration.
[testng] 04:07:45,317 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 04:07:45,318 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:07:45,319 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-26_04-07-45.log]
[testng] 04:07:45,319 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67e8071d - End of configuration.
[testng] 04:08:45,329 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 04:08:45,329 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:08:45,330 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-26_04-08-45.log]
[testng] 04:08:45,330 |-INFO in ch.qos.logback.core.sift.SiftProcessor@774592ad - End of configuration.
[testng] 04:09:23,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 04:09:23,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:09:23,904 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-26_04-09-23.log]
[testng] 04:09:23,905 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b0a803c - End of configuration.
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 901, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 203 minutes 51 seconds
Finished: SUCCESS