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Started by upstream project "BIOFORMATS-test-repo" build number 53 originally caused by: Started by upstream project "Trigger" build number 60 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/jenkins1961912803878934534.sh + '[' leica = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_7680_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] 01:21:14,144 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:21:14,146 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 01:21:14,146 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:21:14,147 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:21:14,148 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:21:14,148 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:21:14,148 |-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] 01:21:14,148 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:21:14,149 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:21:14,149 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:21:14,150 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:21:14,150 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:21:14,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:21:14,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:21:14,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:21:14,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:21:14,341 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:21:14,341 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:21:14,341 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:21:14,342 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:21:14,342 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 01:21:14,342 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 01:21:14,343 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 194 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-04 01:21:14,351] [main] java.version = 11.0.16 [testng] 01:21:14,354 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:21:14,354 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:14,395 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-04_01-21-14.log] [testng] 01:21:14,396 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-05-04 01:21:14,398] [main] testng.directory = /data [testng] [2024-05-04 01:21:14,398] [main] testng.configDirectory = /config [testng] [2024-05-04 01:21:14,407] [main] testng.multiplier = 1.0 [testng] [2024-05-04 01:21:14,409] [main] testng.in-memory = false [testng] [2024-05-04 01:21:14,409] [main] testng.allow-missing = false [testng] [2024-05-04 01:21:14,409] [main] user.language = en [testng] [2024-05-04 01:21:14,409] [main] user.country = ${user.country} [testng] [2024-05-04 01:21:14,409] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-05-04 01:21:29,136] [main] ---------------------------------------- [testng] [2024-05-04 01:21:29,136] [main] Total files: 5651 [testng] [2024-05-04 01:21:29,137] [main] Scan time: 14.727 s (2 ms/file) [testng] [2024-05-04 01:21:29,137] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-04 01:21:45,975] [pool-1-thread-1] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] 01:21:45,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:21:45,976 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:45,978 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-04_01-21-45.log] [testng] 01:21:45,979 |-INFO in ch.qos.logback.core.sift.SiftProcessor@136941eb - End of configuration. [testng] [2024-05-04 01:21:46,046] [pool-1-thread-12] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] 01:21:46,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:21:46,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:46,048 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-04_01-21-46.log] [testng] 01:21:46,048 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8dd0 - End of configuration. [testng] [2024-05-04 01:21:46,175] [pool-1-thread-11] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] 01:21:46,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:21:46,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:46,176 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-04_01-21-46.log] [testng] 01:21:46,176 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bb31681 - End of configuration. [testng] [2024-05-04 01:21:46,447] [pool-1-thread-10] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] 01:21:46,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:21:46,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:46,448 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-04_01-21-46.log] [testng] 01:21:46,449 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32b3bae8 - End of configuration. [testng] [2024-05-04 01:21:46,495] [pool-1-thread-9] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] 01:21:46,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:21:46,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:46,496 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-04_01-21-46.log] [testng] 01:21:46,497 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a8a2531 - End of configuration. [testng] [2024-05-04 01:21:46,562] [pool-1-thread-8] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] 01:21:46,562 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:21:46,562 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:46,563 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-04_01-21-46.log] [testng] 01:21:46,564 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3af73357 - End of configuration. [testng] [2024-05-04 01:21:46,576] [pool-1-thread-7] Initializing /data/samples/Leica_sample.lei: [testng] 01:21:46,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:21:46,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:46,577 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-04_01-21-46.log] [testng] 01:21:46,578 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31f6bbf4 - End of configuration. [testng] [2024-05-04 01:21:46,624] [pool-1-thread-6] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] 01:21:46,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:21:46,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:46,625 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-04_01-21-46.log] [testng] 01:21:46,626 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2941939a - End of configuration. [testng] [2024-05-04 01:21:46,662] [pool-1-thread-5] Initializing /data/constantin/cell6/Logo.jpg: [testng] 01:21:46,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:21:46,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:46,663 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-04_01-21-46.log] [testng] 01:21:46,664 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f7acdd - End of configuration. [testng] [2024-05-04 01:21:46,678] [pool-1-thread-4] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] 01:21:46,678 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:21:46,678 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:46,679 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-04_01-21-46.log] [testng] 01:21:46,679 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1447fb6a - End of configuration. [testng] [2024-05-04 01:21:46,704] [pool-1-thread-3] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] 01:21:46,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:21:46,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:46,705 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-04_01-21-46.log] [testng] 01:21:46,706 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61e42101 - End of configuration. [testng] [2024-05-04 01:21:47,169] [pool-1-thread-2] Initializing /data/david/megan/megan.lei: [testng] 01:21:47,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:21:47,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:47,170 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-04_01-21-47.log] [testng] 01:21:47,171 |-INFO in ch.qos.logback.core.sift.SiftProcessor@485a3526 - End of configuration. [testng] [2024-05-04 01:21:48,539] [pool-1-thread-8] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2024-05-04 01:21:48,622] [pool-1-thread-5] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2024-05-04 01:21:48,672] [pool-1-thread-7] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2024-05-04 01:21:49,133] [pool-1-thread-1] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2024-05-04 01:21:54,758] [pool-1-thread-8] Initializing /data/julie/c164_1.tif: [testng] [2024-05-04 01:21:59,825] [pool-1-thread-8] Initializing /data/clay/leica_stack.tif: [testng] [2024-05-04 01:22:00,169] [pool-1-thread-4] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] [2024-05-04 01:22:00,321] [pool-1-thread-8] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] [2024-05-04 01:22:00,959] [pool-1-thread-8] Initializing /data/brian/leica-original/050118.lei: [testng] [2024-05-04 01:22:01,562] [pool-1-thread-5] Initializing /data/constantin/cell6/cell6.lei: [testng] [2024-05-04 01:22:02,342] [pool-1-thread-6] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] [2024-05-04 01:22:05,480] [pool-1-thread-10] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-05-04 01:22:05,947] [pool-1-thread-10] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] [2024-05-04 01:22:06,106] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2024-05-04 01:22:06,315] [pool-1-thread-10] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-05-04 01:22:08,232] [pool-1-thread-11] Initializing /data/oliver/o459/o459.lei: [testng] [2024-05-04 01:22:10,839] [pool-1-thread-7] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2024-05-04 01:22:12,589] [pool-1-thread-2] Initializing /data/clay/leica_stack.lei: [testng] [2024-05-04 01:22:13,512] [pool-1-thread-2] Initializing /data/brian/tropo/tropo.lei: [testng] [2024-05-04 01:22:13,798] [pool-1-thread-4] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2024-05-04 01:22:14,978] [pool-1-thread-4] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] [2024-05-04 01:22:15,156] [pool-1-thread-4] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-05-04 01:22:15,411] [pool-1-thread-2] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] [2024-05-04 01:22:16,328] [pool-1-thread-2] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2024-05-04 01:22:20,194] [pool-1-thread-9] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] [2024-05-04 01:22:21,642] [pool-1-thread-9] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] [2024-05-04 01:22:21,722] [pool-1-thread-6] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2024-05-04 01:22:21,967] [pool-1-thread-9] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2024-05-04 01:22:22,820] [pool-1-thread-5] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [2024-05-04 01:22:22,981] [pool-1-thread-5] Initializing /data/david/intestine/intestine.lei: [testng] [2024-05-04 01:22:29,069] [pool-1-thread-12] Initializing /data/julie/biorad/25-65.tif: [testng] [2024-05-04 01:22:29,877] [pool-1-thread-12] Initializing /data/constantin/cell6/cell6/Logo.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 32 seconds Finished: SUCCESS