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Started by upstream project "BIOFORMATS-test-repo" build number 389 originally caused by: Started by upstream project "Trigger" build number 412 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/jenkins16065005206509726676.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_61485_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] 00:27:50,474 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:27:50,476 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - No custom configurators were discovered as a service. [testng] 00:27:50,476 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:27:50,477 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:27:50,477 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:27:50,477 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:27:50,478 |-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] 00:27:50,478 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:27:50,478 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:27:50,478 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:27:50,478 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:27:50,479 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:27:50,707 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:27:50,707 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:27:50,736 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:27:50,737 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:27:50,745 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:27:50,745 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:27:50,745 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:27:50,746 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:27:50,746 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@63355449 - End of configuration. [testng] 00:27:50,746 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48ae9b55 - Registering current configuration as safe fallback point [testng] 00:27:50,747 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 269 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-24 00:27:50,756] [main] java.version = 1.8.0_342 [testng] 00:27:50,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:27:50,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:50,806 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-24_00-27-50.log] [testng] 00:27:50,808 |-INFO in ch.qos.logback.core.sift.SiftProcessor@765d7657 - End of configuration. [testng] [2025-03-24 00:27:50,810] [main] testng.directory = /data [testng] [2025-03-24 00:27:50,810] [main] testng.configDirectory = /config [testng] [2025-03-24 00:27:50,822] [main] testng.multiplier = 1.0 [testng] [2025-03-24 00:27:50,823] [main] testng.in-memory = false [testng] [2025-03-24 00:27:50,823] [main] testng.allow-missing = false [testng] [2025-03-24 00:27:50,823] [main] user.language = fr [testng] [2025-03-24 00:27:50,823] [main] user.country = FR [testng] [2025-03-24 00:27:50,823] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2025-03-24 00:28:09,107] [main] ---------------------------------------- [testng] [2025-03-24 00:28:09,107] [main] Total files: 5651 [testng] [2025-03-24 00:28:09,108] [main] Scan time: 18.284 s (3 ms/file) [testng] [2025-03-24 00:28:09,108] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-24 00:28:39,690] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] 00:28:39,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:28:39,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:39,692 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-24_00-28-39.log] [testng] 00:28:39,692 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4cf7828 - End of configuration. [testng] [2025-03-24 00:28:39,772] [pool-1-thread-12] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] 00:28:39,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:28:39,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:39,774 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-24_00-28-39.log] [testng] 00:28:39,774 |-INFO in ch.qos.logback.core.sift.SiftProcessor@663c6e3a - End of configuration. [testng] [2025-03-24 00:28:40,253] [pool-1-thread-11] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] 00:28:40,253 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:28:40,253 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:40,254 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-24_00-28-40.log] [testng] 00:28:40,254 |-INFO in ch.qos.logback.core.sift.SiftProcessor@479783ad - End of configuration. [testng] [2025-03-24 00:28:40,641] [pool-1-thread-10] Initializing /data/julie/c164_1.tif: [testng] 00:28:40,642 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:28:40,642 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:40,642 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-24_00-28-40.log] [testng] 00:28:40,643 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c8b07e9 - End of configuration. [testng] [2025-03-24 00:28:41,687] [pool-1-thread-9] Initializing /data/oliver/o459/o459.lei: [testng] 00:28:41,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:28:41,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:41,688 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-24_00-28-41.log] [testng] 00:28:41,689 |-INFO in ch.qos.logback.core.sift.SiftProcessor@171e6af3 - End of configuration. [testng] [2025-03-24 00:28:42,014] [pool-1-thread-8] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] 00:28:42,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:28:42,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:42,015 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-24_00-28-42.log] [testng] 00:28:42,015 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17d61b52 - End of configuration. [testng] [2025-03-24 00:28:42,371] [pool-1-thread-7] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] 00:28:42,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:28:42,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:42,372 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-24_00-28-42.log] [testng] 00:28:42,372 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62eccc31 - End of configuration. [testng] [2025-03-24 00:28:42,617] [pool-1-thread-6] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] 00:28:42,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:28:42,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:42,618 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-24_00-28-42.log] [testng] 00:28:42,619 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29fc9f02 - End of configuration. [testng] [2025-03-24 00:28:42,656] [pool-1-thread-5] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] 00:28:42,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:28:42,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:42,657 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-24_00-28-42.log] [testng] 00:28:42,658 |-INFO in ch.qos.logback.core.sift.SiftProcessor@375e9d4d - End of configuration. [testng] [2025-03-24 00:28:43,181] [pool-1-thread-4] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] 00:28:43,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:28:43,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:43,182 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-24_00-28-43.log] [testng] 00:28:43,182 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5961066c - End of configuration. [testng] [2025-03-24 00:28:43,503] [pool-1-thread-3] Initializing /data/clay/leica_stack.tif: [testng] 00:28:43,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:28:43,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:43,504 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-24_00-28-43.log] [testng] 00:28:43,504 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bb6111e - End of configuration. [testng] [2025-03-24 00:28:43,768] [pool-1-thread-2] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] 00:28:43,768 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:28:43,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:43,769 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-24_00-28-43.log] [testng] 00:28:43,771 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66f813 - End of configuration. [testng] [2025-03-24 00:28:46,449] [pool-1-thread-1] Initializing /data/brian/tropo/tropo.lei: [testng] [2025-03-24 00:28:47,017] [pool-1-thread-6] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] [2025-03-24 00:28:48,369] [pool-1-thread-3] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] [2025-03-24 00:28:50,442] [pool-1-thread-5] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2025-03-24 00:28:51,604] [pool-1-thread-3] Initializing /data/andrey/10310500/10310500.lei: [testng] [2025-03-24 00:28:54,919] [pool-1-thread-10] Initializing /data/david/intestine/intestine.lei: [testng] [2025-03-24 00:29:04,137] [pool-1-thread-4] Initializing /data/brian/leica-original/050118.lei: [testng] [2025-03-24 00:29:17,383] [pool-1-thread-1] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] [2025-03-24 00:29:51,001] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [2025-03-24 00:29:57,353] [pool-1-thread-1] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] [2025-03-24 00:30:03,211] [pool-1-thread-1] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] [2025-03-24 00:30:19,984] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6.lei: [testng] [2025-03-24 00:34:04,689] [pool-1-thread-12] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2025-03-24 00:34:22,754] [pool-1-thread-6] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2025-03-24 00:34:27,006] [pool-1-thread-6] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] [2025-03-24 00:34:31,047] [pool-1-thread-6] Initializing /data/clay/leica_stack.lei: [testng] [2025-03-24 00:34:53,832] [pool-1-thread-6] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2025-03-24 00:35:07,127] [pool-1-thread-6] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2025-03-24 00:38:48,284] [pool-1-thread-2] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2025-03-24 00:42:00,855] [pool-1-thread-11] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2025-03-24 00:42:09,704] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2025-03-24 00:42:10,530] [pool-1-thread-10] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2025-03-24 00:42:17,593] [pool-1-thread-7] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2025-03-24 00:42:27,936] [pool-1-thread-11] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2025-03-24 00:44:49,686] [pool-1-thread-1] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2025-03-24 00:45:53,214] [pool-1-thread-5] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2025-03-24 00:47:29,246] [pool-1-thread-8] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2025-03-24 00:48:03,090] [pool-1-thread-5] Initializing /data/julie/biorad/25-65.tif: [testng] [2025-03-24 00:48:20,893] [pool-1-thread-5] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2025-03-24 00:49:21,560] [pool-1-thread-4] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2025-03-24 00:50:11,944] [pool-1-thread-1] Initializing /data/david/megan/megan.lei: [testng] [2025-03-24 00:50:55,277] [pool-1-thread-3] Initializing /data/samples/Leica_sample.lei: [testng] 05:46:31,794 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 05:46:31,794 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:46:31,795 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-24_05-46-31.log] [testng] 05:46:31,795 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2181cd98 - End of configuration. [testng] 06:01:18,578 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 06:01:18,578 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:01:18,579 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-24_06-01-18.log] [testng] 06:01:18,580 |-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: 333 minutes 30 seconds Finished: SUCCESS