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Started by upstream project "BIOFORMATS-test-repo" build number 9 originally caused by: Started by upstream project "Trigger" build number 12 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/jenkins4276113574183985540.sh + '[' leica = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_1281_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] 00:19:31,654 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:19:31,656 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 00:19:31,656 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:19:31,657 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:19:31,657 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:19:31,658 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:19:31,658 |-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] 00:19:31,658 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:19:31,658 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:19:31,659 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:19:31,659 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:19:31,660 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:19:31,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:19:31,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:19:31,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:19:31,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:19:31,849 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:19:31,849 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:19:31,850 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:19:31,850 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:19:31,850 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 00:19:31,851 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 00:19:31,851 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 193 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-23 00:19:31,860] [main] java.version = 11.0.16 [testng] 00:19:31,863 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:19:31,863 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:19:31,904 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-23_00-19-31.log] [testng] 00:19:31,905 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-03-23 00:19:31,907] [main] testng.directory = /data [testng] [2024-03-23 00:19:31,907] [main] testng.configDirectory = /config [testng] [2024-03-23 00:19:31,917] [main] testng.multiplier = 1.0 [testng] [2024-03-23 00:19:31,918] [main] testng.in-memory = false [testng] [2024-03-23 00:19:31,918] [main] testng.allow-missing = false [testng] [2024-03-23 00:19:31,918] [main] user.language = en [testng] [2024-03-23 00:19:31,918] [main] user.country = ${user.country} [testng] [2024-03-23 00:19:31,918] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-23 00:19:43,835] [main] ---------------------------------------- [testng] [2024-03-23 00:19:43,835] [main] Total files: 5651 [testng] [2024-03-23 00:19:43,835] [main] Scan time: 11.917 s (2 ms/file) [testng] [2024-03-23 00:19:43,836] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-23 00:20:03,580] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] 00:20:03,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:20:03,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:03,583 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-23_00-20-03.log] [testng] 00:20:03,584 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51946609 - End of configuration. [testng] [2024-03-23 00:20:03,603] [pool-1-thread-12] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] 00:20:03,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:20:03,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:03,604 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-23_00-20-03.log] [testng] 00:20:03,604 |-INFO in ch.qos.logback.core.sift.SiftProcessor@346f37a9 - End of configuration. [testng] [2024-03-23 00:20:03,613] [pool-1-thread-11] Initializing /data/clay/leica_stack.lei: [testng] 00:20:03,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:20:03,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:03,614 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-23_00-20-03.log] [testng] 00:20:03,615 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d51f80a - End of configuration. [testng] [2024-03-23 00:20:03,771] [pool-1-thread-10] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] 00:20:03,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:20:03,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:03,772 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-23_00-20-03.log] [testng] 00:20:03,772 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d7521c7 - End of configuration. [testng] [2024-03-23 00:20:03,870] [pool-1-thread-9] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] 00:20:03,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:20:03,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:03,871 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-23_00-20-03.log] [testng] 00:20:03,871 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d0a4fbd - End of configuration. [testng] [2024-03-23 00:20:03,883] [pool-1-thread-8] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] 00:20:03,884 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:20:03,884 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:03,885 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-23_00-20-03.log] [testng] 00:20:03,885 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28b12c9c - End of configuration. [testng] [2024-03-23 00:20:03,957] [pool-1-thread-7] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] 00:20:03,957 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:20:03,957 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:03,957 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-23_00-20-03.log] [testng] 00:20:03,958 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1447fb6a - End of configuration. [testng] [2024-03-23 00:20:04,172] [pool-1-thread-6] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] 00:20:04,172 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:20:04,172 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:04,173 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-23_00-20-04.log] [testng] 00:20:04,173 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73e8f8cb - End of configuration. [testng] [2024-03-23 00:20:04,592] [pool-1-thread-5] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] 00:20:04,592 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:20:04,592 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:04,593 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-23_00-20-04.log] [testng] 00:20:04,594 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64409c06 - End of configuration. [testng] [2024-03-23 00:20:04,685] [pool-1-thread-4] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] 00:20:04,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:20:04,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:04,685 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-23_00-20-04.log] [testng] 00:20:04,686 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e158a06 - End of configuration. [testng] [2024-03-23 00:20:04,769] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6.lei: [testng] 00:20:04,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:20:04,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:04,770 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-23_00-20-04.log] [testng] 00:20:04,770 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44d16b81 - End of configuration. [testng] [2024-03-23 00:20:04,842] [pool-1-thread-2] Initializing /data/samples/Leica_sample.lei: [testng] 00:20:04,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:20:04,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:04,843 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-23_00-20-04.log] [testng] 00:20:04,843 |-INFO in ch.qos.logback.core.sift.SiftProcessor@351a8d7a - End of configuration. [testng] [2024-03-23 00:20:06,252] [pool-1-thread-12] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2024-03-23 00:20:06,386] [pool-1-thread-1] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-03-23 00:20:06,691] [pool-1-thread-9] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-03-23 00:20:08,018] [pool-1-thread-2] Initializing /data/david/intestine/intestine.lei: [testng] [2024-03-23 00:20:10,294] [pool-1-thread-11] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] [2024-03-23 00:20:11,175] [pool-1-thread-11] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] [2024-03-23 00:20:18,710] [pool-1-thread-11] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2024-03-23 00:20:29,149] [pool-1-thread-12] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2024-03-23 00:20:31,913] [pool-1-thread-12] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] [2024-03-23 00:20:36,321] [pool-1-thread-12] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] [2024-03-23 00:20:41,890] [pool-1-thread-12] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] [2024-03-23 00:21:05,035] [pool-1-thread-10] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2024-03-23 00:21:54,351] [pool-1-thread-8] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-03-23 00:21:55,975] [pool-1-thread-8] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-03-23 00:22:27,425] [pool-1-thread-10] Initializing /data/david/megan/megan.lei: [testng] [2024-03-23 00:22:30,623] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2024-03-23 00:22:31,695] [pool-1-thread-3] Initializing /data/clay/leica_stack.tif: [testng] [2024-03-23 00:22:33,423] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [2024-03-23 00:22:34,665] [pool-1-thread-3] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2024-03-23 00:22:35,018] [pool-1-thread-4] Initializing /data/julie/c164_1.tif: [testng] [2024-03-23 00:22:41,269] [pool-1-thread-4] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2024-03-23 00:22:50,237] [pool-1-thread-2] Initializing /data/julie/biorad/25-65.tif: [testng] [2024-03-23 00:22:51,784] [pool-1-thread-11] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-03-23 00:22:52,572] [pool-1-thread-2] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] [2024-03-23 00:22:53,403] [pool-1-thread-2] Initializing /data/brian/tropo/tropo.lei: [testng] [2024-03-23 00:22:59,393] [pool-1-thread-2] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2024-03-23 00:23:07,761] [pool-1-thread-12] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-03-23 00:23:08,812] [pool-1-thread-12] Initializing /data/oliver/o459/o459.lei: [testng] [2024-03-23 00:23:18,334] [pool-1-thread-8] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2024-03-23 00:23:22,722] [pool-1-thread-9] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2024-03-23 00:23:26,771] [pool-1-thread-3] Initializing /data/brian/leica-original/050118.lei: [testng] [2024-03-23 00:23:33,390] [pool-1-thread-5] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2332, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 14 minutes 10 seconds Finished: SUCCESS