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Started by upstream project "BIOFORMATS-test-repo" build number 357 originally caused by: Started by upstream project "Trigger" build number 383 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/jenkins17147861957768868767.sh + '[' leica = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_56806_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] 00:21:25,109 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:21:25,111 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - No custom configurators were discovered as a service. [testng] 00:21:25,111 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:21:25,112 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:21:25,112 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:21:25,112 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:21:25,113 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:21:25,113 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:21:25,113 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:21:25,114 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:21:25,114 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:21:25,114 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:21:25,274 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:21:25,274 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:21:25,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:21:25,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:21:25,301 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:21:25,301 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:21:25,301 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:21:25,302 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:21:25,302 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@65c7a252 - End of configuration. [testng] 00:21:25,303 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@38cee291 - Registering current configuration as safe fallback point [testng] 00:21:25,303 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 190 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-02-25 00:21:25,311] [main] java.version = 11.0.16 [testng] 00:21:25,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:21:25,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:25,355 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-02-25_00-21-25.log] [testng] 00:21:25,357 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13d73f29 - End of configuration. [testng] [2025-02-25 00:21:25,359] [main] testng.directory = /data [testng] [2025-02-25 00:21:25,359] [main] testng.configDirectory = /config [testng] [2025-02-25 00:21:25,368] [main] testng.multiplier = 1.0 [testng] [2025-02-25 00:21:25,369] [main] testng.in-memory = false [testng] [2025-02-25 00:21:25,369] [main] testng.allow-missing = false [testng] [2025-02-25 00:21:25,369] [main] user.language = en [testng] [2025-02-25 00:21:25,370] [main] user.country = ${user.country} [testng] [2025-02-25 00:21:25,370] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-02-25 00:21:36,184] [main] ---------------------------------------- [testng] [2025-02-25 00:21:36,184] [main] Total files: 5651 [testng] [2025-02-25 00:21:36,184] [main] Scan time: 10.814 s (1 ms/file) [testng] [2025-02-25 00:21:36,184] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-02-25 00:21:54,997] [pool-1-thread-1] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] 00:21:54,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:21:54,999 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:55,001 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-02-25_00-21-55.log] [testng] 00:21:55,002 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14cce66 - End of configuration. [testng] [2025-02-25 00:21:55,156] [pool-1-thread-12] Initializing /data/brian/tropo/tropo.lei: [testng] 00:21:55,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:21:55,157 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:55,158 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-02-25_00-21-55.log] [testng] 00:21:55,158 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ce6eb86 - End of configuration. [testng] [2025-02-25 00:21:55,304] [pool-1-thread-11] Initializing /data/simon/Leica demo/test/test.lei: [testng] 00:21:55,304 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:21:55,304 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:55,305 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-02-25_00-21-55.log] [testng] 00:21:55,305 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ac016c1 - End of configuration. [testng] [2025-02-25 00:21:55,480] [pool-1-thread-10] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] 00:21:55,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:21:55,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:55,481 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-02-25_00-21-55.log] [testng] 00:21:55,482 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a05838c - End of configuration. [testng] [2025-02-25 00:21:55,962] [pool-1-thread-9] Initializing /data/julie/biorad/25-65.tif: [testng] 00:21:55,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:21:55,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:55,962 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-02-25_00-21-55.log] [testng] 00:21:55,963 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5feaebee - End of configuration. [testng] [2025-02-25 00:21:56,272] [pool-1-thread-8] Initializing /data/constantin/cell6/cell6.lei: [testng] 00:21:56,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:21:56,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:56,273 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-02-25_00-21-56.log] [testng] 00:21:56,274 |-INFO in ch.qos.logback.core.sift.SiftProcessor@308713c1 - End of configuration. [testng] [2025-02-25 00:21:56,490] [pool-1-thread-7] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] 00:21:56,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:21:56,491 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:56,491 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-02-25_00-21-56.log] [testng] 00:21:56,491 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37c28ad0 - End of configuration. [testng] [2025-02-25 00:21:56,744] [pool-1-thread-6] Initializing /data/samples/Leica_sample.lei: [testng] 00:21:56,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:21:56,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:56,746 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-02-25_00-21-56.log] [testng] 00:21:56,746 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30f49136 - End of configuration. [testng] [2025-02-25 00:21:56,926] [pool-1-thread-5] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] 00:21:56,926 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:21:56,926 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:56,927 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-02-25_00-21-56.log] [testng] 00:21:56,927 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37442984 - End of configuration. [testng] [2025-02-25 00:21:56,959] [pool-1-thread-4] Initializing /data/clay/leica_stack.tif: [testng] 00:21:56,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:21:56,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:56,959 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-02-25_00-21-56.log] [testng] 00:21:56,960 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72d2c450 - End of configuration. [testng] [2025-02-25 00:21:57,118] [pool-1-thread-3] Initializing /data/vytas/4voxels/4voxels.lei: [testng] 00:21:57,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:21:57,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:57,119 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-02-25_00-21-57.log] [testng] 00:21:57,119 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3602da08 - End of configuration. [testng] [2025-02-25 00:21:57,333] [pool-1-thread-2] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] 00:21:57,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:21:57,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:57,334 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-02-25_00-21-57.log] [testng] 00:21:57,334 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7924674 - End of configuration. [testng] [2025-02-25 00:21:59,389] [pool-1-thread-5] Initializing /data/julie/c164_1.tif: [testng] [2025-02-25 00:22:01,020] [pool-1-thread-4] Initializing /data/andrey/10310500/10310500.lei: [testng] [2025-02-25 00:22:02,377] [pool-1-thread-9] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2025-02-25 00:22:03,951] [pool-1-thread-6] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] [2025-02-25 00:22:06,006] [pool-1-thread-1] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] [2025-02-25 00:22:06,781] [pool-1-thread-5] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] [2025-02-25 00:22:08,290] [pool-1-thread-5] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2025-02-25 00:22:09,460] [pool-1-thread-12] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2025-02-25 00:22:11,827] [pool-1-thread-12] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2025-02-25 00:22:17,295] [pool-1-thread-6] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2025-02-25 00:22:18,557] [pool-1-thread-12] Initializing /data/oliver/o459/o459.lei: [testng] [2025-02-25 00:22:59,105] [pool-1-thread-5] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] [2025-02-25 00:23:01,889] [pool-1-thread-5] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2025-02-25 00:23:04,207] [pool-1-thread-5] Initializing /data/david/intestine/intestine.lei: [testng] [2025-02-25 00:23:58,902] [pool-1-thread-9] Initializing /data/brian/leica-original/050118.lei: [testng] [2025-02-25 00:24:06,782] [pool-1-thread-7] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2025-02-25 00:26:35,496] [pool-1-thread-8] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] [2025-02-25 00:26:43,093] [pool-1-thread-2] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2025-02-25 00:26:45,374] [pool-1-thread-7] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2025-02-25 00:26:47,312] [pool-1-thread-8] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2025-02-25 00:26:48,931] [pool-1-thread-2] Initializing /data/clay/leica_stack.lei: [testng] [2025-02-25 00:26:55,051] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2025-02-25 00:26:56,481] [pool-1-thread-7] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2025-02-25 00:27:00,466] [pool-1-thread-1] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] [2025-02-25 00:27:07,494] [pool-1-thread-2] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2025-02-25 00:27:10,024] [pool-1-thread-2] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2025-02-25 00:27:48,332] [pool-1-thread-5] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2025-02-25 00:28:07,341] [pool-1-thread-11] Initializing /data/david/megan/megan.lei: [testng] [2025-02-25 00:28:37,574] [pool-1-thread-6] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2025-02-25 00:29:20,365] [pool-1-thread-2] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2025-02-25 00:29:22,341] [pool-1-thread-5] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2025-02-25 00:29:31,861] [pool-1-thread-4] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2332, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 33 minutes 32 seconds Finished: SUCCESS