Started by upstream project "BIOFORMATS-test-repo" build number 203
originally caused by:
Started by upstream project "Trigger" build number 229
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@10
[BIOFORMATS-test-folder@10] $ /bin/bash -xe /tmp/jenkins13747738833749501874.sh
+ '[' perkinelmer-operetta = slidebook ']'
++ date +%u
+ '[' 6 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_32163_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] 01:34:23,173 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:34:23,175 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service.
[testng] 01:34:23,175 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:34:23,176 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:34:23,176 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:34:23,177 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:34:23,177 |-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] 01:34:23,177 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:34:23,177 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:34:23,178 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:34:23,178 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:34:23,179 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:34:23,375 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:34:23,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:34:23,400 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:34:23,400 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:34:23,415 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:34:23,415 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:34:23,415 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:34:23,416 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:34:23,416 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration.
[testng] 01:34:23,417 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point
[testng] 01:34:23,417 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 240 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-09-28 01:34:23,427] [main] java.version = 11.0.16
[testng] 01:34:23,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:34:23,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:34:23,474 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-28_01-34-23.log]
[testng] 01:34:23,475 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
[testng] [2024-09-28 01:34:23,478] [main] testng.directory = /data
[testng] [2024-09-28 01:34:23,479] [main] testng.configDirectory = /config
[testng] [2024-09-28 01:34:23,489] [main] testng.multiplier = 1.0
[testng] [2024-09-28 01:34:23,491] [main] testng.in-memory = false
[testng] [2024-09-28 01:34:23,491] [main] testng.allow-missing = false
[testng] [2024-09-28 01:34:23,491] [main] user.language = en
[testng] [2024-09-28 01:34:23,491] [main] user.country = ${user.country}
[testng] [2024-09-28 01:34:23,491] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-09-28 01:39:56,940] [main] ----------------------------------------
[testng] [2024-09-28 01:39:56,940] [main] Total files: 14663
[testng] [2024-09-28 01:39:56,940] [main] Scan time: 333.449 s (22 ms/file)
[testng] [2024-09-28 01:39:56,941] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 16 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-09-28 01:42:43,658] [pool-1-thread-1] Initializing /data/public/idr0034/HipSci Experiment 10 Plate 1__2014-08-21T17_57_35-Measurement1/Images/Index.idx.xml:
[testng] 01:42:43,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:42:43,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:42:43,661 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-28_01-42-43.log]
[testng] 01:42:43,661 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1fb0b0a6 - End of configuration.
[testng] [2024-09-28 01:42:47,923] [pool-1-thread-12] Initializing /data/samples/no-first-series/Index.idx.xml:
[testng] 01:42:47,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:42:47,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:42:47,925 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-28_01-42-47.log]
[testng] 01:42:47,925 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41c47090 - End of configuration.
[testng] [2024-09-28 01:42:48,149] [pool-1-thread-11] Initializing /data/public/omer/006P_M3/006P_M3_overview_fields.png:
[testng] 01:42:48,150 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:42:48,150 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:42:48,150 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-28_01-42-48.log]
[testng] 01:42:48,151 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4263be58 - End of configuration.
[testng] [2024-09-28 01:42:48,182] [pool-1-thread-10] Initializing /data/stephen/P004-CC Edu-pHH3__2009-02-03T17_36_29-Measurement1/Images/Index.idx.xml:
[testng] 01:42:48,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:42:48,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:42:48,183 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-28_01-42-48.log]
[testng] 01:42:48,183 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26a72d17 - End of configuration.
[testng] [2024-09-28 01:42:48,599] [pool-1-thread-9] Initializing /data/hms/ryang_skbr3_p1__2012-07-10T15_24_30-Measurement1/Images/Index.idx.xml:
[testng] 01:42:48,599 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:42:48,599 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:42:48,600 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-28_01-42-48.log]
[testng] 01:42:48,600 |-INFO in ch.qos.logback.core.sift.SiftProcessor@cbc603f - End of configuration.
[testng] [2024-09-28 01:42:48,872] [pool-1-thread-8] Initializing /data/samples/new-phenix/artificial-v6/Hiplex_run1_cycle1_MsPos/Index.idx.xml:
[testng] 01:42:48,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:42:48,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:42:48,873 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-28_01-42-48.log]
[testng] 01:42:48,873 |-INFO in ch.qos.logback.core.sift.SiftProcessor@505188f - End of configuration.
[testng] [2024-09-28 01:42:49,670] [pool-1-thread-7] Initializing /data/pki/Export/HRMNY-13786__2021-11-23T13_44_30-Measurement 3/Images/Index.xml:
[testng] 01:42:49,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:42:49,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:42:49,671 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-28_01-42-49.log]
[testng] 01:42:49,671 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bc3d4fa - End of configuration.
[testng] [2024-09-28 01:42:50,323] [pool-1-thread-6] Initializing /data/public/zenodo-7841360/Hoechst__2023-03-07T10_17_54-Measurement 2/Images/Index.idx.xml:
[testng] 01:42:50,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:42:50,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:42:50,323 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-28_01-42-50.log]
[testng] 01:42:50,324 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73577b11 - End of configuration.
[testng] [2024-09-28 01:42:50,571] [pool-1-thread-5] Initializing /data/public/omer/006P_M3/006P__2017-08-19T12_42_59-Measurement 3/Images/Index.idx.xml:
[testng] 01:42:50,571 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:42:50,571 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:42:50,572 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-28_01-42-50.log]
[testng] 01:42:50,572 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27015304 - End of configuration.
[testng] [2024-09-28 01:42:51,228] [pool-1-thread-4] Initializing /data/qa-17826/JLM-20170801-Operetta/Index.idx.xml:
[testng] 01:42:51,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:42:51,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:42:51,229 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-28_01-42-51.log]
[testng] 01:42:51,229 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77dcec0b - End of configuration.
[testng] [2024-09-28 01:42:51,596] [pool-1-thread-3] Initializing /data/stephen/Plate 1(2)__2011-09-29T23_50_20-Measurement1/Images/Index.idx.xml:
[testng] 01:42:51,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:42:51,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:42:51,597 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-28_01-42-51.log]
[testng] 01:42:51,597 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2228e4d1 - End of configuration.
[testng] [2024-09-28 01:42:51,907] [pool-1-thread-2] Initializing /data/samples/32-bit-file/Index.idx.xml:
[testng] 01:42:51,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:42:51,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:42:51,907 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-28_01-42-51.log]
[testng] 01:42:51,908 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61384096 - End of configuration.
[testng] [2024-09-28 01:42:53,639] [pool-1-thread-11] Initializing /data/samples/smaller-xy/Index.idx.xml:
[testng] [2024-09-28 01:42:57,905] [pool-1-thread-6] Initializing /data/public/omer/006P_M3/006P_M3_overview.png:
[testng] [2024-09-28 01:42:58,903] [pool-1-thread-6] Initializing /data/pki/DataSet/dec61bf8-5ca8-415a-8639-b75bf59ca47c/images/index.xml:
[testng] [2024-09-28 01:43:15,915] [pool-1-thread-9] Initializing /data/samples/new-phenix/original/Hiplex_run1_cycle1_MsPos/Index.idx.xml:
[testng] 03:08:29,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 03:08:29,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:08:29,922 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-28_03-08-29.log]
[testng] 03:08:29,923 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35e4f1af - End of configuration.
[testng] 03:16:41,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 03:16:41,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:16:41,921 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-28_03-16-41.log]
[testng] 03:16:41,921 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a644009 - End of configuration.
[testng] 03:17:04,270 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 03:17:04,271 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:17:04,272 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-28_03-17-04.log]
[testng] 03:17:04,273 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b37ba43 - End of configuration.
[testng] 03:17:24,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 03:17:24,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:17:24,220 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-28_03-17-24.log]
[testng] 03:17:24,220 |-INFO in ch.qos.logback.core.sift.SiftProcessor@beb6a12 - 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: 103 minutes 4 seconds
Finished: SUCCESS