Started by upstream project "BIOFORMATS-test-repo" build number 263
originally caused by:
Started by user devspace
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3
[BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins15314871536350700622.sh
+ '[' perkinelmer-operetta = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_41487_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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release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] 15:47:30,192 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 15:47:30,193 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service.
[testng] 15:47:30,193 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 15:47:30,194 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 15:47:30,194 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 15:47:30,195 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 15:47:30,195 |-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] 15:47:30,195 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 15:47:30,195 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 15:47:30,196 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 15:47:30,196 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 15:47:30,197 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 15:47:30,355 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 15:47:30,355 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 15:47:30,381 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 15:47:30,381 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 15:47:30,388 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 15:47:30,388 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 15:47:30,388 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 15:47:30,388 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 15:47:30,388 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration.
[testng] 15:47:30,389 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point
[testng] 15:47:30,389 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 194 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-11-21 15:47:30,399] [main] java.version = 21
[testng] 15:47:30,402 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 15:47:30,402 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 15:47:30,444 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-21_15-47-30.log]
[testng] 15:47:30,445 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration.
[testng] [2024-11-21 15:47:30,447] [main] testng.directory = /data
[testng] [2024-11-21 15:47:30,447] [main] testng.configDirectory = /config
[testng] [2024-11-21 15:47:30,456] [main] testng.multiplier = 1.0
[testng] [2024-11-21 15:47:30,456] [main] testng.in-memory = false
[testng] [2024-11-21 15:47:30,456] [main] testng.allow-missing = false
[testng] [2024-11-21 15:47:30,456] [main] user.language = en
[testng] [2024-11-21 15:47:30,456] [main] user.country = ${user.country}
[testng] [2024-11-21 15:47:30,456] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-11-21 16:00:32,166] [main] ----------------------------------------
[testng] [2024-11-21 16:00:32,166] [main] Total files: 14681
[testng] [2024-11-21 16:00:32,167] [main] Scan time: 781.71 s (53 ms/file)
[testng] [2024-11-21 16:00:32,167] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 17 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-11-21 16:21:33,242] [pool-1-thread-1] Initializing /data/qa-17826/JLM-20170801-Operetta/Index.idx.xml:
[testng] 16:21:33,242 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 16:21:33,243 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 16:21:33,244 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-21_16-21-33.log]
[testng] 16:21:33,244 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d9ae73 - End of configuration.
[testng] [2024-11-21 16:21:34,632] [pool-1-thread-12] Initializing /data/samples/extra-directories/Index.idx.xml:
[testng] 16:21:34,632 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 16:21:34,632 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 16:21:34,633 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-21_16-21-34.log]
[testng] 16:21:34,633 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5cd5fa79 - End of configuration.
[testng] [2024-11-21 16:21:36,098] [pool-1-thread-11] Initializing /data/samples/no-first-series/Index.idx.xml:
[testng] 16:21:36,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 16:21:36,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 16:21:36,099 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-21_16-21-36.log]
[testng] 16:21:36,100 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ec45fcb - End of configuration.
[testng] [2024-11-21 16:21:37,533] [pool-1-thread-10] Initializing /data/pki/DataSet/dec61bf8-5ca8-415a-8639-b75bf59ca47c/images/index.xml:
[testng] 16:21:37,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 16:21:37,534 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 16:21:37,535 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-21_16-21-37.log]
[testng] 16:21:37,535 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2eccac63 - End of configuration.
[testng] [2024-11-21 16:21:39,702] [pool-1-thread-9] Initializing /data/public/omer/006P_M3/006P_M3_overview.png:
[testng] 16:21:39,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 16:21:39,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 16:21:39,703 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-21_16-21-39.log]
[testng] 16:21:39,704 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fa03425 - End of configuration.
[testng] [2024-11-21 16:21:39,781] [pool-1-thread-8] Initializing /data/samples/new-phenix/artificial-v6/Hiplex_run1_cycle1_MsPos/Index.idx.xml:
[testng] 16:21:39,781 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 16:21:39,781 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 16:21:39,782 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-21_16-21-39.log]
[testng] 16:21:39,782 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38f94840 - End of configuration.
[testng] [2024-11-21 16:21:42,887] [pool-1-thread-7] Initializing /data/public/omer/006P_M3/006P__2017-08-19T12_42_59-Measurement 3/Images/Index.idx.xml:
[testng] 16:21:42,887 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 16:21:42,887 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 16:21:42,887 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-21_16-21-42.log]
[testng] 16:21:42,888 |-INFO in ch.qos.logback.core.sift.SiftProcessor@176b6f5e - End of configuration.
[testng] [2024-11-21 16:21:50,629] [pool-1-thread-6] Initializing /data/hms/ryang_skbr3_p1__2012-07-10T15_24_30-Measurement1/Images/Index.idx.xml:
[testng] 16:21:50,630 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 16:21:50,630 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 16:21:50,631 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-21_16-21-50.log]
[testng] 16:21:50,631 |-INFO in ch.qos.logback.core.sift.SiftProcessor@185dbddc - End of configuration.
[testng] [2024-11-21 16:21:51,980] [pool-1-thread-5] Initializing /data/samples/new-phenix/original/Hiplex_run1_cycle1_MsPos/Index.idx.xml:
[testng] 16:21:51,980 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 16:21:51,980 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 16:21:51,981 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-21_16-21-51.log]
[testng] 16:21:51,981 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77e243ac - End of configuration.
[testng] [2024-11-21 16:22:00,325] [pool-1-thread-4] Initializing /data/public/omer/006P_M3/006P_M3_overview_fields.png:
[testng] 16:22:00,325 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 16:22:00,325 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 16:22:00,326 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-21_16-22-00.log]
[testng] 16:22:00,326 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f25b784 - End of configuration.
[testng] [2024-11-21 16:22:00,400] [pool-1-thread-3] Initializing /data/stephen/Plate 1(2)__2011-09-29T23_50_20-Measurement1/Images/Index.idx.xml:
[testng] 16:22:00,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 16:22:00,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 16:22:00,401 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-21_16-22-00.log]
[testng] 16:22:00,402 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12518c7b - End of configuration.
[testng] [2024-11-21 16:22:01,804] [pool-1-thread-2] Initializing /data/stephen/P004-CC Edu-pHH3__2009-02-03T17_36_29-Measurement1/Images/Index.idx.xml:
[testng] 16:22:01,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 16:22:01,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 16:22:01,805 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-21_16-22-01.log]
[testng] 16:22:01,805 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5564314d - End of configuration.
[testng] [2024-11-21 16:22:07,784] [pool-1-thread-4] Initializing /data/samples/32-bit-file/Index.idx.xml:
[testng] [2024-11-21 16:22:09,859] [pool-1-thread-9] Initializing /data/public/idr0034/HipSci Experiment 10 Plate 1__2014-08-21T17_57_35-Measurement1/Images/Index.idx.xml:
[testng] [2024-11-21 16:23:24,336] [pool-1-thread-11] Initializing /data/public/zenodo-7841360/Hoechst__2023-03-07T10_17_54-Measurement 2/Images/Index.idx.xml:
[testng] [2024-11-21 16:23:25,443] [pool-1-thread-6] Initializing /data/pki/Export/HRMNY-13786__2021-11-23T13_44_30-Measurement 3/Images/Index.xml:
[testng] [2024-11-21 16:23:29,872] [pool-1-thread-1] Initializing /data/samples/smaller-xy/Index.idx.xml:
[testng] 18:52:57,647 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 18:52:57,647 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 18:52:57,648 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-21_18-52-57.log]
[testng] 18:52:57,648 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37773bbb - End of configuration.
[testng] 19:14:44,094 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 19:14:44,094 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 19:14:44,095 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-21_19-14-44.log]
[testng] 19:14:44,095 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6159be07 - End of configuration.
[testng] 19:14:44,555 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 19:14:44,555 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 19:14:44,556 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-21_19-14-44.log]
[testng] 19:14:44,556 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3246e984 - End of configuration.
[testng] 19:15:04,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 19:15:04,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 19:15:04,431 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-21_19-15-04.log]
[testng] 19:15:04,431 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51d8ce52 - 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: 207 minutes 37 seconds
Finished: SUCCESS