Started by upstream project "BIOFORMATS-test-repo" build number 67
originally caused by:
Started by upstream project "Trigger" build number 75
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/jenkins7265655237103413790.sh
+ '[' leica = slidebook ']'
++ date +%u
+ '[' 6 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_9976_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] 01:21:11,855 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:21:11,857 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service.
[testng] 01:21:11,857 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:21:11,858 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:21:11,858 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:21:11,859 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:21:11,859 |-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] 01:21:11,859 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:21:11,859 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:21:11,860 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:21:11,860 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:21:11,861 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:21:12,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:21:12,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:21:12,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:21:12,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:21:12,052 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:21:12,052 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:21:12,052 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:21:12,053 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:21:12,053 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration.
[testng] 01:21:12,054 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point
[testng] 01:21:12,054 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 195 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-05-18 01:21:12,062] [main] java.version = 11.0.16
[testng] 01:21:12,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:21:12,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:12,106 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-18_01-21-12.log]
[testng] 01:21:12,108 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
[testng] [2024-05-18 01:21:12,110] [main] testng.directory = /data
[testng] [2024-05-18 01:21:12,111] [main] testng.configDirectory = /config
[testng] [2024-05-18 01:21:12,121] [main] testng.multiplier = 1.0
[testng] [2024-05-18 01:21:12,122] [main] testng.in-memory = false
[testng] [2024-05-18 01:21:12,122] [main] testng.allow-missing = false
[testng] [2024-05-18 01:21:12,122] [main] user.language = en
[testng] [2024-05-18 01:21:12,122] [main] user.country = ${user.country}
[testng] [2024-05-18 01:21:12,122] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-05-18 01:21:23,693] [main] ----------------------------------------
[testng] [2024-05-18 01:21:23,694] [main] Total files: 5651
[testng] [2024-05-18 01:21:23,694] [main] Scan time: 11.571 s (2 ms/file)
[testng] [2024-05-18 01:21:23,695] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 44 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-05-18 01:21:37,260] [pool-1-thread-1] Initializing /data/constantin/cell6/Graphs_1_00.jpg:
[testng] 01:21:37,261 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:21:37,261 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:37,263 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-18_01-21-37.log]
[testng] 01:21:37,264 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b03c16f - End of configuration.
[testng] [2024-05-18 01:21:37,284] [pool-1-thread-12] Initializing /data/brian/leica-original/050118.lei:
[testng] 01:21:37,284 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:21:37,284 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:37,285 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-18_01-21-37.log]
[testng] 01:21:37,285 |-INFO in ch.qos.logback.core.sift.SiftProcessor@306f6444 - End of configuration.
[testng] [2024-05-18 01:21:37,623] [pool-1-thread-11] Initializing /data/martin/samples-SP2/samples-SP2.lei:
[testng] 01:21:37,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:21:37,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:37,625 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-18_01-21-37.log]
[testng] 01:21:37,625 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6489b886 - End of configuration.
[testng] [2024-05-18 01:21:37,659] [pool-1-thread-10] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif:
[testng] 01:21:37,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:21:37,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:37,660 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-18_01-21-37.log]
[testng] 01:21:37,660 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10a737f7 - End of configuration.
[testng] [2024-05-18 01:21:37,723] [pool-1-thread-9] Initializing /data/vytas/4voxels/4voxels.lei:
[testng] 01:21:37,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:21:37,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:37,724 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-18_01-21-37.log]
[testng] 01:21:37,724 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3efe8769 - End of configuration.
[testng] [2024-05-18 01:21:37,773] [pool-1-thread-8] Initializing /data/mark/071026-561nm check/071026-561nm check.lei:
[testng] 01:21:37,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:21:37,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:37,774 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-18_01-21-37.log]
[testng] 01:21:37,774 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59ca39eb - End of configuration.
[testng] [2024-05-18 01:21:37,858] [pool-1-thread-7] Initializing /data/grant/Leica SP2 (25-11-10).lei:
[testng] 01:21:37,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:21:37,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:37,859 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-18_01-21-37.log]
[testng] 01:21:37,860 |-INFO in ch.qos.logback.core.sift.SiftProcessor@439612 - End of configuration.
[testng] [2024-05-18 01:21:37,904] [pool-1-thread-6] Initializing /data/stjude/NIHSSE02-3.lei:
[testng] 01:21:37,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:21:37,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:37,905 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-18_01-21-37.log]
[testng] 01:21:37,906 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a8a2531 - End of configuration.
[testng] [2024-05-18 01:21:37,945] [pool-1-thread-5] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei:
[testng] 01:21:37,945 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:21:37,945 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:37,946 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-18_01-21-37.log]
[testng] 01:21:37,946 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2941939a - End of configuration.
[testng] [2024-05-18 01:21:38,018] [pool-1-thread-4] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg:
[testng] 01:21:38,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:21:38,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:38,019 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-18_01-21-38.log]
[testng] 01:21:38,019 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f7acdd - End of configuration.
[testng] [2024-05-18 01:21:38,026] [pool-1-thread-3] Initializing /data/constantin/cell6/Quant_Image_00.jpg:
[testng] 01:21:38,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:21:38,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:38,027 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-18_01-21-38.log]
[testng] 01:21:38,028 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e158a06 - End of configuration.
[testng] [2024-05-18 01:21:38,034] [pool-1-thread-2] Initializing /data/julie/c164_1.tif:
[testng] 01:21:38,035 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:21:38,035 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:38,035 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-18_01-21-38.log]
[testng] 01:21:38,036 |-INFO in ch.qos.logback.core.sift.SiftProcessor@355e6db5 - End of configuration.
[testng] [2024-05-18 01:21:39,340] [pool-1-thread-4] Initializing /data/clay/leica_stack.tif:
[testng] [2024-05-18 01:21:39,364] [pool-1-thread-3] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei:
[testng] [2024-05-18 01:21:39,518] [pool-1-thread-1] Initializing /data/oliver/o459/o459.lei:
[testng] [2024-05-18 01:21:39,737] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6/Logo.jpg:
[testng] [2024-05-18 01:21:39,907] [pool-1-thread-4] Initializing /data/constantin/cell6/Quant_Image_01.jpg:
[testng] [2024-05-18 01:21:39,916] [pool-1-thread-10] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei:
[testng] [2024-05-18 01:21:40,185] [pool-1-thread-4] Initializing /data/julie/biorad/25-65.tif:
[testng] [2024-05-18 01:21:40,648] [pool-1-thread-10] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei:
[testng] [2024-05-18 01:21:41,164] [pool-1-thread-4] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg:
[testng] [2024-05-18 01:21:41,400] [pool-1-thread-4] Initializing /data/constantin/cell6/cell6.lei:
[testng] [2024-05-18 01:21:43,408] [pool-1-thread-2] Initializing /data/brian/050627-leica/050628-leica.lei:
[testng] [2024-05-18 01:21:44,889] [pool-1-thread-6] Initializing /data/joel/sequential scan 2/sequential scan 2.lei:
[testng] [2024-05-18 01:21:51,370] [pool-1-thread-5] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei:
[testng] [2024-05-18 01:21:54,689] [pool-1-thread-11] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif:
[testng] [2024-05-18 01:21:55,636] [pool-1-thread-11] Initializing /data/simon/Leica demo/test/test.lei:
[testng] [2024-05-18 01:21:55,889] [pool-1-thread-3] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei:
[testng] [2024-05-18 01:22:00,167] [pool-1-thread-10] Initializing /data/constantin/cell6/Quant_Image_02.jpg:
[testng] [2024-05-18 01:22:00,331] [pool-1-thread-8] Initializing /data/clay/leica_stack.lei:
[testng] [2024-05-18 01:22:00,360] [pool-1-thread-10] Initializing /data/brian/tropo/tropo.lei:
[testng] [2024-05-18 01:22:01,091] [pool-1-thread-8] Initializing /data/constantin/cell6/Logo.jpg:
[testng] [2024-05-18 01:22:01,199] [pool-1-thread-8] Initializing /data/david/intestine/intestine.lei:
[testng] [2024-05-18 01:22:01,630] [pool-1-thread-4] Initializing /data/michael/2007-01-31_zres_sp2.lei:
[testng] [2024-05-18 01:22:01,810] [pool-1-thread-10] Initializing /data/simon/Leica demo/fish/fish.lei:
[testng] [2024-05-18 01:22:03,291] [pool-1-thread-4] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg:
[testng] [2024-05-18 01:22:03,525] [pool-1-thread-4] Initializing /data/samples/Leica_sample.lei:
[testng] [2024-05-18 01:22:04,180] [pool-1-thread-4] Initializing /data/christophe/Leica stacks/Nf5.lei:
[testng] [2024-05-18 01:22:06,587] [pool-1-thread-6] Initializing /data/joel/sequential scan 3/sequential scan 3.lei:
[testng] [2024-05-18 01:22:12,323] [pool-1-thread-7] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei:
[testng] [2024-05-18 01:22:18,249] [pool-1-thread-4] Initializing /data/julie/biorad/8291mcd8_raw01.pic:
[testng] [2024-05-18 01:22:19,212] [pool-1-thread-4] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei:
[testng] [2024-05-18 01:22:23,566] [pool-1-thread-11] Initializing /data/david/megan/megan.lei:
[testng] [2024-05-18 01:22:24,308] [pool-1-thread-7] Initializing /data/andrey/10310500/10310500.lei:
[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 33 seconds
Finished: SUCCESS