Started by upstream project "BIOFORMATS-test-repo" build number 104
originally caused by:
Started by upstream project "Trigger" build number 116
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder
[BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins18235490341364622723.sh
+ '[' leica = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_16044_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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release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] 01:21:16,586 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:21:16,587 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service.
[testng] 01:21:16,587 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:21:16,588 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:21:16,588 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:21:16,589 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:21:16,589 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:21:16,589 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:21:16,589 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:21:16,590 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:21:16,590 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:21:16,590 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:21:16,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:21:16,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:21:16,777 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:21:16,777 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:21:16,782 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:21:16,782 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:21:16,782 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:21:16,783 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:21:16,783 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration.
[testng] 01:21:16,784 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point
[testng] 01:21:16,784 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 195 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-06-27 01:21:16,792] [main] java.version = 21
[testng] 01:21:16,795 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:21:16,795 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:16,834 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-27_01-21-16.log]
[testng] 01:21:16,835 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration.
[testng] [2024-06-27 01:21:16,837] [main] testng.directory = /data
[testng] [2024-06-27 01:21:16,837] [main] testng.configDirectory = /config
[testng] [2024-06-27 01:21:16,845] [main] testng.multiplier = 1.0
[testng] [2024-06-27 01:21:16,846] [main] testng.in-memory = false
[testng] [2024-06-27 01:21:16,846] [main] testng.allow-missing = false
[testng] [2024-06-27 01:21:16,846] [main] user.language = en
[testng] [2024-06-27 01:21:16,846] [main] user.country = ${user.country}
[testng] [2024-06-27 01:21:16,846] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-06-27 01:21:33,290] [main] ----------------------------------------
[testng] [2024-06-27 01:21:33,290] [main] Total files: 5651
[testng] [2024-06-27 01:21:33,290] [main] Scan time: 16.443 s (2 ms/file)
[testng] [2024-06-27 01:21:33,291] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 44 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-06-27 01:21:51,336] [pool-1-thread-1] Initializing /data/samples/Leica_sample.lei:
[testng] 01:21:51,337 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:21:51,337 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:51,338 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-27_01-21-51.log]
[testng] 01:21:51,338 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4344d6ef - End of configuration.
[testng] [2024-06-27 01:21:51,373] [pool-1-thread-12] Initializing /data/david/intestine/intestine.lei:
[testng] 01:21:51,373 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:21:51,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:51,374 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-27_01-21-51.log]
[testng] 01:21:51,375 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a2944df - End of configuration.
[testng] [2024-06-27 01:21:51,404] [pool-1-thread-11] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei:
[testng] 01:21:51,404 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:21:51,404 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:51,405 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-27_01-21-51.log]
[testng] 01:21:51,405 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f8b68cf - End of configuration.
[testng] [2024-06-27 01:21:51,419] [pool-1-thread-10] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei:
[testng] 01:21:51,420 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:21:51,420 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:51,420 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-27_01-21-51.log]
[testng] 01:21:51,421 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32d4d3f3 - End of configuration.
[testng] [2024-06-27 01:21:51,506] [pool-1-thread-9] Initializing /data/clay/leica_stack.tif:
[testng] 01:21:51,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:21:51,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:51,507 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-27_01-21-51.log]
[testng] 01:21:51,508 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d883d08 - End of configuration.
[testng] [2024-06-27 01:21:51,530] [pool-1-thread-8] Initializing /data/martin/samples-SP2/samples-SP2.lei:
[testng] 01:21:51,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:21:51,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:51,531 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-27_01-21-51.log]
[testng] 01:21:51,531 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5651f6be - End of configuration.
[testng] [2024-06-27 01:21:51,669] [pool-1-thread-7] Initializing /data/stjude/NIHSSE02-3.lei:
[testng] 01:21:51,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:21:51,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:51,671 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-27_01-21-51.log]
[testng] 01:21:51,671 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ff7e647 - End of configuration.
[testng] [2024-06-27 01:21:51,718] [pool-1-thread-6] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif:
[testng] 01:21:51,719 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:21:51,719 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:51,719 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-27_01-21-51.log]
[testng] 01:21:51,720 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63b98082 - End of configuration.
[testng] [2024-06-27 01:21:51,769] [pool-1-thread-5] Initializing /data/grant/Leica SP2 (25-11-10).lei:
[testng] 01:21:51,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:21:51,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:51,770 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-27_01-21-51.log]
[testng] 01:21:51,771 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75e34d1f - End of configuration.
[testng] [2024-06-27 01:21:51,816] [pool-1-thread-4] Initializing /data/constantin/cell6/cell6/Logo.jpg:
[testng] 01:21:51,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:21:51,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:51,817 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-27_01-21-51.log]
[testng] 01:21:51,817 |-INFO in ch.qos.logback.core.sift.SiftProcessor@744df4f1 - End of configuration.
[testng] [2024-06-27 01:21:51,824] [pool-1-thread-3] Initializing /data/julie/biorad/8291mcd8_raw01.pic:
[testng] 01:21:51,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:21:51,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:51,825 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-27_01-21-51.log]
[testng] 01:21:51,826 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50c899be - End of configuration.
[testng] [2024-06-27 01:21:51,859] [pool-1-thread-2] Initializing /data/joel/sequential scan 3/sequential scan 3.lei:
[testng] 01:21:51,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:21:51,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:51,860 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-27_01-21-51.log]
[testng] 01:21:51,861 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1668e4cb - End of configuration.
[testng] [2024-06-27 01:21:53,109] [pool-1-thread-4] Initializing /data/brian/leica-original/050118.lei:
[testng] [2024-06-27 01:21:53,525] [pool-1-thread-1] Initializing /data/clay/leica_stack.lei:
[testng] [2024-06-27 01:21:53,557] [pool-1-thread-9] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei:
[testng] [2024-06-27 01:21:53,639] [pool-1-thread-11] Initializing /data/joel/sequential scan 2/sequential scan 2.lei:
[testng] [2024-06-27 01:21:53,743] [pool-1-thread-3] Initializing /data/constantin/cell6/Quant_Image_01.jpg:
[testng] [2024-06-27 01:21:53,991] [pool-1-thread-6] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei:
[testng] [2024-06-27 01:21:54,226] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg:
[testng] [2024-06-27 01:21:54,429] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg:
[testng] [2024-06-27 01:21:54,612] [pool-1-thread-3] Initializing /data/julie/c164_1.tif:
[testng] [2024-06-27 01:21:55,109] [pool-1-thread-1] Initializing /data/simon/Leica demo/fish/fish.lei:
[testng] [2024-06-27 01:21:57,917] [pool-1-thread-7] Initializing /data/constantin/cell6/Quant_Image_00.jpg:
[testng] [2024-06-27 01:21:58,100] [pool-1-thread-7] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif:
[testng] [2024-06-27 01:21:58,902] [pool-1-thread-7] Initializing /data/andrey/10310500/10310500.lei:
[testng] [2024-06-27 01:21:59,647] [pool-1-thread-3] Initializing /data/christophe/Leica stacks/Nf5.lei:
[testng] [2024-06-27 01:22:06,079] [pool-1-thread-9] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg:
[testng] [2024-06-27 01:22:06,280] [pool-1-thread-9] Initializing /data/david/megan/megan.lei:
[testng] [2024-06-27 01:22:07,543] [pool-1-thread-8] Initializing /data/brian/050627-leica/050628-leica.lei:
[testng] [2024-06-27 01:22:10,602] [pool-1-thread-2] Initializing /data/constantin/cell6/Quant_Image_02.jpg:
[testng] [2024-06-27 01:22:10,807] [pool-1-thread-2] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei:
[testng] [2024-06-27 01:22:10,886] [pool-1-thread-3] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei:
[testng] [2024-06-27 01:22:12,424] [pool-1-thread-11] Initializing /data/michael/2007-01-31_zres_sp2.lei:
[testng] [2024-06-27 01:22:13,706] [pool-1-thread-11] Initializing /data/brian/tropo/tropo.lei:
[testng] [2024-06-27 01:22:15,254] [pool-1-thread-11] Initializing /data/mark/071026-561nm check/071026-561nm check.lei:
[testng] [2024-06-27 01:22:19,445] [pool-1-thread-5] Initializing /data/simon/Leica demo/test/test.lei:
[testng] [2024-06-27 01:22:22,852] [pool-1-thread-2] Initializing /data/constantin/cell6/cell6.lei:
[testng] [2024-06-27 01:22:24,640] [pool-1-thread-12] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei:
[testng] [2024-06-27 01:22:26,662] [pool-1-thread-9] Initializing /data/constantin/cell6/Logo.jpg:
[testng] [2024-06-27 01:22:26,830] [pool-1-thread-9] Initializing /data/oliver/o459/o459.lei:
[testng] [2024-06-27 01:22:28,943] [pool-1-thread-10] Initializing /data/vytas/4voxels/4voxels.lei:
[testng] [2024-06-27 01:22:29,577] [pool-1-thread-3] Initializing /data/julie/biorad/25-65.tif:
[testng] [2024-06-27 01:22:30,188] [pool-1-thread-3] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei:
[testng] [2024-06-27 01:22:32,388] [pool-1-thread-11] Initializing /data/constantin/cell6/Graphs_1_00.jpg:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 2332, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 3 minutes 27 seconds
Finished: SUCCESS