Started by upstream project "BIOFORMATS-test-repo" build number 382
originally caused by:
Started by upstream project "Trigger" build number 404
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4
[BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins13838921849388345285.sh
+ '[' leica = slidebook ']'
++ date +%u
+ '[' 2 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_60390_merge_ci -v /uod/idr/repos/curated/leica:/data -v /uod/idr-scratch/merge-ci/curated/leica:/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] 00:23:26,764 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15
[testng] 00:23:26,766 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - No custom configurators were discovered as a service.
[testng] 00:23:26,766 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:23:26,767 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:23:26,767 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 00:23:26,768 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 00:23:26,768 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 00:23:26,768 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:23:26,769 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:23:26,769 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 00:23:26,770 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 00:23:26,770 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 00:23:26,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 00:23:26,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 00:23:26,971 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 00:23:26,971 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 00:23:26,977 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 00:23:26,977 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 00:23:26,977 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 00:23:26,977 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 00:23:26,977 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@65c7a252 - End of configuration.
[testng] 00:23:26,978 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@38cee291 - Registering current configuration as safe fallback point
[testng] 00:23:26,978 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 209 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2025-03-18 00:23:26,988] [main] java.version = 11.0.16
[testng] 00:23:26,991 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 00:23:26,991 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:23:27,034 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-18_00-23-27.log]
[testng] 00:23:27,036 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13d73f29 - End of configuration.
[testng] [2025-03-18 00:23:27,038] [main] testng.directory = /data
[testng] [2025-03-18 00:23:27,038] [main] testng.configDirectory = /config
[testng] [2025-03-18 00:23:27,048] [main] testng.multiplier = 1.0
[testng] [2025-03-18 00:23:27,049] [main] testng.in-memory = false
[testng] [2025-03-18 00:23:27,049] [main] testng.allow-missing = false
[testng] [2025-03-18 00:23:27,049] [main] user.language = en
[testng] [2025-03-18 00:23:27,050] [main] user.country = ${user.country}
[testng] [2025-03-18 00:23:27,050] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2025-03-18 00:25:17,998] [main] ----------------------------------------
[testng] [2025-03-18 00:25:17,998] [main] Total files: 5651
[testng] [2025-03-18 00:25:17,998] [main] Scan time: 110.948 s (19 ms/file)
[testng] [2025-03-18 00:25:17,998] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 44 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2025-03-18 00:28:44,273] [pool-1-thread-1] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei:
[testng] 00:28:44,274 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 00:28:44,274 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:28:44,276 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-18_00-28-44.log]
[testng] 00:28:44,276 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2570a868 - End of configuration.
[testng] [2025-03-18 00:28:45,022] [pool-1-thread-12] Initializing /data/brian/tropo/tropo.lei:
[testng] 00:28:45,023 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 00:28:45,023 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:28:45,024 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-18_00-28-45.log]
[testng] 00:28:45,024 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c4a44c1 - End of configuration.
[testng] [2025-03-18 00:28:45,871] [pool-1-thread-11] Initializing /data/simon/Leica demo/test/test.lei:
[testng] 00:28:45,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 00:28:45,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:28:45,872 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-18_00-28-45.log]
[testng] 00:28:45,873 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8b7167d - End of configuration.
[testng] [2025-03-18 00:28:46,915] [pool-1-thread-10] Initializing /data/simon/Leica demo/fish/fish.lei:
[testng] 00:28:46,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 00:28:46,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:28:46,916 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-18_00-28-46.log]
[testng] 00:28:46,916 |-INFO in ch.qos.logback.core.sift.SiftProcessor@560d1612 - End of configuration.
[testng] [2025-03-18 00:28:48,271] [pool-1-thread-9] Initializing /data/julie/biorad/25-65.tif:
[testng] 00:28:48,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 00:28:48,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:28:48,272 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-18_00-28-48.log]
[testng] 00:28:48,273 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7af77a99 - End of configuration.
[testng] [2025-03-18 00:28:49,640] [pool-1-thread-8] Initializing /data/constantin/cell6/cell6.lei:
[testng] 00:28:49,640 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 00:28:49,640 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:28:49,641 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-18_00-28-49.log]
[testng] 00:28:49,641 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1299d2f9 - End of configuration.
[testng] [2025-03-18 00:28:50,523] [pool-1-thread-7] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei:
[testng] 00:28:50,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 00:28:50,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:28:50,524 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-18_00-28-50.log]
[testng] 00:28:50,524 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57346058 - End of configuration.
[testng] [2025-03-18 00:28:51,417] [pool-1-thread-6] Initializing /data/samples/Leica_sample.lei:
[testng] 00:28:51,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 00:28:51,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:28:51,418 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-18_00-28-51.log]
[testng] 00:28:51,419 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d5c161f - End of configuration.
[testng] [2025-03-18 00:28:52,155] [pool-1-thread-5] Initializing /data/constantin/cell6/Quant_Image_02.jpg:
[testng] 00:28:52,155 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 00:28:52,155 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:28:52,156 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-18_00-28-52.log]
[testng] 00:28:52,156 |-INFO in ch.qos.logback.core.sift.SiftProcessor@114ea78e - End of configuration.
[testng] [2025-03-18 00:28:52,266] [pool-1-thread-4] Initializing /data/clay/leica_stack.tif:
[testng] 00:28:52,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 00:28:52,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:28:52,267 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-18_00-28-52.log]
[testng] 00:28:52,268 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78acad29 - End of configuration.
[testng] [2025-03-18 00:28:53,041] [pool-1-thread-3] Initializing /data/vytas/4voxels/4voxels.lei:
[testng] 00:28:53,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 00:28:53,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:28:53,041 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-18_00-28-53.log]
[testng] 00:28:53,042 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1691469e - End of configuration.
[testng] [2025-03-18 00:28:53,888] [pool-1-thread-2] Initializing /data/joel/sequential scan 3/sequential scan 3.lei:
[testng] 00:28:53,888 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 00:28:53,888 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:28:53,889 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-18_00-28-53.log]
[testng] 00:28:53,889 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3693f75d - End of configuration.
[testng] [2025-03-18 00:29:00,659] [pool-1-thread-5] Initializing /data/julie/c164_1.tif:
[testng] [2025-03-18 00:29:04,951] [pool-1-thread-4] Initializing /data/andrey/10310500/10310500.lei:
[testng] [2025-03-18 00:29:09,011] [pool-1-thread-9] Initializing /data/christophe/Leica stacks/Nf5.lei:
[testng] [2025-03-18 00:29:13,096] [pool-1-thread-6] Initializing /data/michael/2007-01-31_zres_sp2.lei:
[testng] [2025-03-18 00:29:18,275] [pool-1-thread-5] Initializing /data/martin/samples-SP2/samples-SP2.lei:
[testng] [2025-03-18 00:29:21,191] [pool-1-thread-1] Initializing /data/constantin/cell6/Quant_Image_00.jpg:
[testng] [2025-03-18 00:29:25,457] [pool-1-thread-1] Initializing /data/stjude/NIHSSE02-3.lei:
[testng] [2025-03-18 00:29:34,972] [pool-1-thread-12] Initializing /data/constantin/cell6/Graphs_1_00.jpg:
[testng] [2025-03-18 00:29:42,734] [pool-1-thread-12] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif:
[testng] [2025-03-18 00:30:06,570] [pool-1-thread-6] Initializing /data/grant/Leica SP2 (25-11-10).lei:
[testng] [2025-03-18 00:30:18,433] [pool-1-thread-12] Initializing /data/oliver/o459/o459.lei:
[testng] [2025-03-18 00:34:06,094] [pool-1-thread-1] Initializing /data/constantin/cell6/Quant_Image_01.jpg:
[testng] [2025-03-18 00:34:11,814] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg:
[testng] [2025-03-18 00:34:17,784] [pool-1-thread-1] Initializing /data/david/intestine/intestine.lei:
[testng] [2025-03-18 00:42:11,324] [pool-1-thread-9] Initializing /data/brian/leica-original/050118.lei:
[testng] [2025-03-18 00:43:49,396] [pool-1-thread-7] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei:
[testng] [2025-03-18 00:51:32,909] [pool-1-thread-7] Initializing /data/julie/biorad/8291mcd8_raw01.pic:
[testng] [2025-03-18 00:51:38,804] [pool-1-thread-8] Initializing /data/constantin/cell6/Logo.jpg:
[testng] [2025-03-18 00:51:44,586] [pool-1-thread-8] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif:
[testng] [2025-03-18 00:51:57,838] [pool-1-thread-2] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei:
[testng] [2025-03-18 00:52:03,066] [pool-1-thread-7] Initializing /data/clay/leica_stack.lei:
[testng] [2025-03-18 00:52:08,165] [pool-1-thread-8] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg:
[testng] [2025-03-18 00:52:15,683] [pool-1-thread-8] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei:
[testng] [2025-03-18 00:52:24,399] [pool-1-thread-5] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei:
[testng] [2025-03-18 00:52:45,771] [pool-1-thread-7] Initializing /data/constantin/cell6/cell6/Logo.jpg:
[testng] [2025-03-18 00:52:51,973] [pool-1-thread-7] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei:
[testng] [2025-03-18 00:54:27,327] [pool-1-thread-1] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei:
[testng] [2025-03-18 00:56:07,173] [pool-1-thread-11] Initializing /data/david/megan/megan.lei:
[testng] [2025-03-18 00:57:51,771] [pool-1-thread-6] Initializing /data/brian/050627-leica/050628-leica.lei:
[testng] [2025-03-18 01:00:14,637] [pool-1-thread-1] Initializing /data/joel/sequential scan 2/sequential scan 2.lei:
[testng] [2025-03-18 01:00:32,545] [pool-1-thread-4] Initializing /data/mark/071026-561nm check/071026-561nm check.lei:
[testng] [2025-03-18 01:00:37,256] [pool-1-thread-7] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg:
[testng] 05:39:43,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 05:39:43,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 05:39:43,845 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-18_05-39-43.log]
[testng] 05:39:43,846 |-INFO in ch.qos.logback.core.sift.SiftProcessor@294a12b5 - End of configuration.
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 2332, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 316 minutes 20 seconds
Finished: SUCCESS