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Started by upstream project "BIOFORMATS-test-repo" build number 381 originally caused by: Started by upstream project "Trigger" build number 403 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins13827322035705176298.sh + '[' leica = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_60225_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 -Duser.language=fr -Duser.country=FR 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 test-automated: [testng] File leak detector installed [testng] 01:27:30,244 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 01:27:30,246 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - No custom configurators were discovered as a service. [testng] 01:27:30,246 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:27:30,247 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:27:30,248 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:27:30,248 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:27:30,248 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:27:30,248 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:27:30,249 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:27:30,249 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:27:30,249 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:27:30,249 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:27:30,476 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:27:30,476 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:27:30,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:27:30,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:27:30,513 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:27:30,513 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:27:30,513 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:27:30,514 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:27:30,514 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@63355449 - End of configuration. [testng] 01:27:30,515 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48ae9b55 - Registering current configuration as safe fallback point [testng] 01:27:30,515 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 266 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-17 01:27:30,524] [main] java.version = 1.8.0_342 [testng] 01:27:30,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:27:30,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:30,573 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-17_01-27-30.log] [testng] 01:27:30,575 |-INFO in ch.qos.logback.core.sift.SiftProcessor@765d7657 - End of configuration. [testng] [2025-03-17 01:27:30,577] [main] testng.directory = /data [testng] [2025-03-17 01:27:30,578] [main] testng.configDirectory = /config [testng] [2025-03-17 01:27:30,590] [main] testng.multiplier = 1.0 [testng] [2025-03-17 01:27:30,591] [main] testng.in-memory = false [testng] [2025-03-17 01:27:30,591] [main] testng.allow-missing = false [testng] [2025-03-17 01:27:30,591] [main] user.language = fr [testng] [2025-03-17 01:27:30,591] [main] user.country = FR [testng] [2025-03-17 01:27:30,591] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2025-03-17 01:29:32,752] [main] ---------------------------------------- [testng] [2025-03-17 01:29:32,752] [main] Total files: 5651 [testng] [2025-03-17 01:29:32,752] [main] Scan time: 122.161 s (21 ms/file) [testng] [2025-03-17 01:29:32,752] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-17 01:32:44,796] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] 01:32:44,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:32:44,797 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:44,797 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-17_01-32-44.log] [testng] 01:32:44,798 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2961c6b5 - End of configuration. [testng] [2025-03-17 01:32:44,971] [pool-1-thread-12] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] 01:32:44,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:32:44,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:44,972 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-17_01-32-44.log] [testng] 01:32:44,973 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ad309b - End of configuration. [testng] [2025-03-17 01:32:46,676] [pool-1-thread-11] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] 01:32:46,676 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:32:46,676 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:46,677 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-17_01-32-46.log] [testng] 01:32:46,678 |-INFO in ch.qos.logback.core.sift.SiftProcessor@682fdf6c - End of configuration. [testng] [2025-03-17 01:32:48,038] [pool-1-thread-10] Initializing /data/julie/c164_1.tif: [testng] 01:32:48,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:32:48,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:48,039 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-17_01-32-48.log] [testng] 01:32:48,040 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f228622 - End of configuration. [testng] [2025-03-17 01:32:49,750] [pool-1-thread-9] Initializing /data/oliver/o459/o459.lei: [testng] 01:32:49,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:32:49,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:49,750 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-17_01-32-49.log] [testng] 01:32:49,751 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1985ffc8 - End of configuration. [testng] [2025-03-17 01:32:51,065] [pool-1-thread-8] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] 01:32:51,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:32:51,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:51,065 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-17_01-32-51.log] [testng] 01:32:51,066 |-INFO in ch.qos.logback.core.sift.SiftProcessor@141dc6ac - End of configuration. [testng] [2025-03-17 01:32:52,490] [pool-1-thread-7] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] 01:32:52,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:32:52,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:52,490 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-17_01-32-52.log] [testng] 01:32:52,491 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11fe2e53 - End of configuration. [testng] [2025-03-17 01:32:53,965] [pool-1-thread-6] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] 01:32:53,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:32:53,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:53,965 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-17_01-32-53.log] [testng] 01:32:53,966 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71582800 - End of configuration. [testng] [2025-03-17 01:32:54,170] [pool-1-thread-5] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] 01:32:54,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:32:54,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:54,170 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-17_01-32-54.log] [testng] 01:32:54,171 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f94596 - End of configuration. [testng] [2025-03-17 01:32:56,797] [pool-1-thread-4] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] 01:32:56,797 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:32:56,797 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:56,798 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-17_01-32-56.log] [testng] 01:32:56,798 |-INFO in ch.qos.logback.core.sift.SiftProcessor@304e43b1 - End of configuration. [testng] [2025-03-17 01:32:58,612] [pool-1-thread-3] Initializing /data/clay/leica_stack.tif: [testng] 01:32:58,612 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:32:58,612 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:58,613 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-17_01-32-58.log] [testng] 01:32:58,613 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f4c8953 - End of configuration. [testng] [2025-03-17 01:33:01,006] [pool-1-thread-2] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] 01:33:01,007 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:33:01,007 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:01,007 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-17_01-33-01.log] [testng] 01:33:01,008 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c15bd59 - End of configuration. [testng] [2025-03-17 01:33:12,750] [pool-1-thread-1] Initializing /data/brian/tropo/tropo.lei: [testng] [2025-03-17 01:33:14,514] [pool-1-thread-6] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] [2025-03-17 01:33:24,471] [pool-1-thread-3] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] [2025-03-17 01:33:29,266] [pool-1-thread-10] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2025-03-17 01:33:32,735] [pool-1-thread-5] Initializing /data/andrey/10310500/10310500.lei: [testng] [2025-03-17 01:33:39,503] [pool-1-thread-3] Initializing /data/david/intestine/intestine.lei: [testng] [2025-03-17 01:34:11,486] [pool-1-thread-4] Initializing /data/brian/leica-original/050118.lei: [testng] [2025-03-17 01:34:30,180] [pool-1-thread-1] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] [2025-03-17 01:35:21,951] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [2025-03-17 01:35:32,734] [pool-1-thread-1] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] [2025-03-17 01:35:44,782] [pool-1-thread-1] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] [2025-03-17 01:36:31,701] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6.lei: [testng] [2025-03-17 01:43:31,637] [pool-1-thread-12] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2025-03-17 01:44:03,402] [pool-1-thread-6] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2025-03-17 01:44:09,436] [pool-1-thread-6] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] [2025-03-17 01:44:16,080] [pool-1-thread-6] Initializing /data/clay/leica_stack.lei: [testng] [2025-03-17 01:44:51,745] [pool-1-thread-6] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2025-03-17 01:45:09,986] [pool-1-thread-6] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2025-03-17 01:48:21,857] [pool-1-thread-2] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2025-03-17 01:51:31,832] [pool-1-thread-3] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2025-03-17 01:51:40,594] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2025-03-17 01:51:41,902] [pool-1-thread-11] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2025-03-17 01:51:49,576] [pool-1-thread-3] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2025-03-17 01:51:54,557] [pool-1-thread-7] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2025-03-17 01:54:22,769] [pool-1-thread-1] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2025-03-17 01:55:14,865] [pool-1-thread-10] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2025-03-17 01:57:33,800] [pool-1-thread-8] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2025-03-17 01:58:26,285] [pool-1-thread-10] Initializing /data/julie/biorad/25-65.tif: [testng] [2025-03-17 01:58:48,973] [pool-1-thread-10] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2025-03-17 02:00:09,400] [pool-1-thread-4] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2025-03-17 02:03:12,324] [pool-1-thread-1] Initializing /data/david/megan/megan.lei: [testng] [2025-03-17 02:04:35,652] [pool-1-thread-5] Initializing /data/samples/Leica_sample.lei: [testng] 05:51:00,390 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 05:51:00,390 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:51:00,391 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-17_05-51-00.log] [testng] 05:51:00,391 |-INFO in ch.qos.logback.core.sift.SiftProcessor@205f7f07 - End of configuration. [testng] 06:03:27,205 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 06:03:27,205 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:03:27,206 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-17_06-03-27.log] [testng] 06:03:27,207 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55202ba6 - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2332, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 275 minutes 59 seconds Finished: SUCCESS