Started by upstream project "BIOFORMATS-test-repo" build number 363 originally caused by: Started by upstream project "Trigger" build number 389 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/jenkins1992439297503927644.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_57796_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] 00:22:25,706 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:22:25,708 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - No custom configurators were discovered as a service. [testng] 00:22:25,708 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:22:25,709 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:22:25,709 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:22:25,709 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:22:25,710 |-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] 00:22:25,710 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:22:25,710 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:22:25,710 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:22:25,711 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:22:25,711 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:22:25,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:22:25,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:22:25,970 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:22:25,970 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:22:25,978 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:22:25,978 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:22:25,979 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:22:25,979 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:22:25,979 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@63355449 - End of configuration. [testng] 00:22:25,980 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48ae9b55 - Registering current configuration as safe fallback point [testng] 00:22:25,980 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 270 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-03 00:22:25,990] [main] java.version = 1.8.0_342 [testng] 00:22:25,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:22:25,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:26,040 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-03_00-22-26.log] [testng] 00:22:26,041 |-INFO in ch.qos.logback.core.sift.SiftProcessor@765d7657 - End of configuration. [testng] [2025-03-03 00:22:26,043] [main] testng.directory = /data [testng] [2025-03-03 00:22:26,043] [main] testng.configDirectory = /config [testng] [2025-03-03 00:22:26,056] [main] testng.multiplier = 1.0 [testng] [2025-03-03 00:22:26,056] [main] testng.in-memory = false [testng] [2025-03-03 00:22:26,056] [main] testng.allow-missing = false [testng] [2025-03-03 00:22:26,057] [main] user.language = fr [testng] [2025-03-03 00:22:26,057] [main] user.country = FR [testng] [2025-03-03 00:22:26,057] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2025-03-03 00:22:44,001] [main] ---------------------------------------- [testng] [2025-03-03 00:22:44,002] [main] Total files: 5651 [testng] [2025-03-03 00:22:44,002] [main] Scan time: 17.944 s (3 ms/file) [testng] [2025-03-03 00:22:44,002] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-03 00:23:14,452] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] 00:23:14,453 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:23:14,453 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:14,454 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-03_00-23-14.log] [testng] 00:23:14,454 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1718a201 - End of configuration. [testng] [2025-03-03 00:23:14,516] [pool-1-thread-12] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] 00:23:14,517 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:23:14,517 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:14,518 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-03_00-23-14.log] [testng] 00:23:14,519 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e079c8e - End of configuration. [testng] [2025-03-03 00:23:15,367] [pool-1-thread-11] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] 00:23:15,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:23:15,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:15,368 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-03_00-23-15.log] [testng] 00:23:15,369 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b92bf18 - End of configuration. [testng] [2025-03-03 00:23:15,628] [pool-1-thread-10] Initializing /data/julie/c164_1.tif: [testng] 00:23:15,628 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:23:15,629 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:15,629 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-03_00-23-15.log] [testng] 00:23:15,630 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b39a7ff - End of configuration. [testng] [2025-03-03 00:23:16,385] [pool-1-thread-9] Initializing /data/oliver/o459/o459.lei: [testng] 00:23:16,385 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:23:16,385 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:16,386 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-03_00-23-16.log] [testng] 00:23:16,386 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18824d58 - End of configuration. [testng] [2025-03-03 00:23:16,659] [pool-1-thread-8] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] 00:23:16,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:23:16,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:16,660 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-03_00-23-16.log] [testng] 00:23:16,660 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71b250d2 - End of configuration. [testng] [2025-03-03 00:23:16,973] [pool-1-thread-7] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] 00:23:16,974 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:23:16,974 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:16,974 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-03_00-23-16.log] [testng] 00:23:16,975 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4172db03 - End of configuration. [testng] [2025-03-03 00:23:17,271] [pool-1-thread-6] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] 00:23:17,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:23:17,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:17,272 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-03_00-23-17.log] [testng] 00:23:17,273 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c4c2c95 - End of configuration. [testng] [2025-03-03 00:23:17,297] [pool-1-thread-5] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] 00:23:17,298 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:23:17,298 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:17,298 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-03_00-23-17.log] [testng] 00:23:17,298 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7af09468 - End of configuration. [testng] [2025-03-03 00:23:18,146] [pool-1-thread-4] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] 00:23:18,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:23:18,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:18,147 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-03_00-23-18.log] [testng] 00:23:18,147 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42db89e9 - End of configuration. [testng] [2025-03-03 00:23:18,429] [pool-1-thread-3] Initializing /data/clay/leica_stack.tif: [testng] 00:23:18,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:23:18,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:18,433 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-03_00-23-18.log] [testng] 00:23:18,434 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24dad4d8 - End of configuration. [testng] [2025-03-03 00:23:18,566] [pool-1-thread-2] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] 00:23:18,566 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:23:18,566 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:18,567 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-03_00-23-18.log] [testng] 00:23:18,567 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31cc57a7 - End of configuration. [testng] [2025-03-03 00:23:21,050] [pool-1-thread-1] Initializing /data/brian/tropo/tropo.lei: [testng] [2025-03-03 00:23:21,577] [pool-1-thread-6] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] [2025-03-03 00:23:22,977] [pool-1-thread-3] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] [2025-03-03 00:23:24,774] [pool-1-thread-5] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2025-03-03 00:23:25,389] [pool-1-thread-3] Initializing /data/andrey/10310500/10310500.lei: [testng] [2025-03-03 00:23:27,800] [pool-1-thread-10] Initializing /data/david/intestine/intestine.lei: [testng] [2025-03-03 00:23:31,245] [pool-1-thread-4] Initializing /data/brian/leica-original/050118.lei: [testng] [2025-03-03 00:23:38,028] [pool-1-thread-1] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] [2025-03-03 00:23:49,206] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [2025-03-03 00:23:51,299] [pool-1-thread-1] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] [2025-03-03 00:23:53,401] [pool-1-thread-1] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] [2025-03-03 00:24:03,455] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6.lei: [testng] [2025-03-03 00:25:28,593] [pool-1-thread-6] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2025-03-03 00:25:30,012] [pool-1-thread-12] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2025-03-03 00:25:31,673] [pool-1-thread-12] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] [2025-03-03 00:25:33,237] [pool-1-thread-12] Initializing /data/clay/leica_stack.lei: [testng] [2025-03-03 00:25:44,806] [pool-1-thread-12] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2025-03-03 00:25:50,783] [pool-1-thread-12] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2025-03-03 00:26:46,419] [pool-1-thread-2] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2025-03-03 00:27:30,231] [pool-1-thread-11] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2025-03-03 00:27:31,921] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2025-03-03 00:27:32,941] [pool-1-thread-7] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2025-03-03 00:27:34,013] [pool-1-thread-11] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2025-03-03 00:27:40,930] [pool-1-thread-10] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2025-03-03 00:28:09,685] [pool-1-thread-1] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2025-03-03 00:28:23,288] [pool-1-thread-5] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2025-03-03 00:28:48,961] [pool-1-thread-8] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2025-03-03 00:28:57,667] [pool-1-thread-5] Initializing /data/julie/biorad/25-65.tif: [testng] [2025-03-03 00:29:03,064] [pool-1-thread-5] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2025-03-03 00:29:37,354] [pool-1-thread-1] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2025-03-03 00:30:01,493] [pool-1-thread-4] Initializing /data/david/megan/megan.lei: [testng] [2025-03-03 00:30:09,089] [pool-1-thread-3] Initializing /data/samples/Leica_sample.lei: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2332, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 25 minutes 50 seconds Finished: SUCCESS