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Started by upstream project "BIOFORMATS-test-repo" build number 69 originally caused by: Started by upstream project "Trigger" build number 77 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/jenkins13141564754352319159.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_10304_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] 01:21:15,252 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:21:15,254 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 01:21:15,254 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:21:15,255 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:21:15,255 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:21:15,255 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:21:15,255 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:21:15,255 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:21:15,256 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:21:15,256 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:21:15,256 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:21:15,256 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:21:15,474 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:21:15,474 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:21:15,501 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:21:15,501 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:21:15,513 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:21:15,513 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:21:15,513 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:21:15,514 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:21:15,514 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 01:21:15,515 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 01:21:15,515 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 259 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-20 01:21:15,524] [main] java.version = 1.8.0_342 [testng] 01:21:15,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:21:15,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:15,571 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-20_01-21-15.log] [testng] 01:21:15,572 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-05-20 01:21:15,574] [main] testng.directory = /data [testng] [2024-05-20 01:21:15,574] [main] testng.configDirectory = /config [testng] [2024-05-20 01:21:15,586] [main] testng.multiplier = 1.0 [testng] [2024-05-20 01:21:15,586] [main] testng.in-memory = false [testng] [2024-05-20 01:21:15,586] [main] testng.allow-missing = false [testng] [2024-05-20 01:21:15,586] [main] user.language = fr [testng] [2024-05-20 01:21:15,586] [main] user.country = FR [testng] [2024-05-20 01:21:15,586] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-05-20 01:21:27,231] [main] ---------------------------------------- [testng] [2024-05-20 01:21:27,231] [main] Total files: 5651 [testng] [2024-05-20 01:21:27,232] [main] Scan time: 11.645 s (2 ms/file) [testng] [2024-05-20 01:21:27,232] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-20 01:21:45,633] [pool-1-thread-1] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] 01:21:45,634 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:21:45,634 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:45,635 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-20_01-21-45.log] [testng] 01:21:45,635 |-INFO in ch.qos.logback.core.sift.SiftProcessor@399940da - End of configuration. [testng] [2024-05-20 01:21:45,675] [pool-1-thread-12] Initializing /data/samples/Leica_sample.lei: [testng] 01:21:45,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:21:45,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:45,676 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-20_01-21-45.log] [testng] 01:21:45,676 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67bd6526 - End of configuration. [testng] [2024-05-20 01:21:45,695] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] 01:21:45,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:21:45,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:45,696 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-20_01-21-45.log] [testng] 01:21:45,696 |-INFO in ch.qos.logback.core.sift.SiftProcessor@84ea091 - End of configuration. [testng] [2024-05-20 01:21:45,704] [pool-1-thread-10] Initializing /data/simon/Leica demo/test/test.lei: [testng] 01:21:45,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:21:45,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:45,705 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-20_01-21-45.log] [testng] 01:21:45,705 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44c24172 - End of configuration. [testng] [2024-05-20 01:21:45,803] [pool-1-thread-9] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] 01:21:45,803 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:21:45,803 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:45,804 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-20_01-21-45.log] [testng] 01:21:45,804 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1fac20f8 - End of configuration. [testng] [2024-05-20 01:21:45,865] [pool-1-thread-8] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] 01:21:45,865 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:21:45,865 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:45,865 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-20_01-21-45.log] [testng] 01:21:45,866 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b5fcb5a - End of configuration. [testng] [2024-05-20 01:21:45,900] [pool-1-thread-7] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] 01:21:45,900 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:21:45,900 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:45,901 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-20_01-21-45.log] [testng] 01:21:45,902 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b8aa549 - End of configuration. [testng] [2024-05-20 01:21:45,910] [pool-1-thread-6] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] 01:21:45,910 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:21:45,910 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:45,911 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-20_01-21-45.log] [testng] 01:21:45,911 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18907a68 - End of configuration. [testng] [2024-05-20 01:21:45,918] [pool-1-thread-5] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] 01:21:45,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:21:45,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:45,919 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-20_01-21-45.log] [testng] 01:21:45,919 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79b3ff03 - End of configuration. [testng] [2024-05-20 01:21:45,943] [pool-1-thread-4] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] 01:21:45,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:21:45,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:45,944 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-20_01-21-45.log] [testng] 01:21:45,945 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53047347 - End of configuration. [testng] [2024-05-20 01:21:45,980] [pool-1-thread-3] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] 01:21:45,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:21:45,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:45,981 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-20_01-21-45.log] [testng] 01:21:45,982 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a88ae3e - End of configuration. [testng] [2024-05-20 01:21:46,302] [pool-1-thread-2] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] 01:21:46,302 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:21:46,302 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:46,303 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-20_01-21-46.log] [testng] 01:21:46,303 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27f13f80 - End of configuration. [testng] [2024-05-20 01:21:47,481] [pool-1-thread-7] Initializing /data/david/megan/megan.lei: [testng] [2024-05-20 01:21:47,522] [pool-1-thread-11] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2024-05-20 01:21:47,572] [pool-1-thread-6] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2024-05-20 01:21:47,644] [pool-1-thread-12] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2024-05-20 01:21:47,674] [pool-1-thread-1] Initializing /data/julie/c164_1.tif: [testng] [2024-05-20 01:21:48,224] [pool-1-thread-2] Initializing /data/constantin/cell6/cell6.lei: [testng] [2024-05-20 01:21:49,832] [pool-1-thread-11] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-05-20 01:21:50,195] [pool-1-thread-11] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-05-20 01:21:54,569] [pool-1-thread-1] Initializing /data/clay/leica_stack.tif: [testng] [2024-05-20 01:21:55,061] [pool-1-thread-1] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2024-05-20 01:21:55,100] [pool-1-thread-12] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2024-05-20 01:21:55,272] [pool-1-thread-12] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-05-20 01:21:55,796] [pool-1-thread-12] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2024-05-20 01:21:59,888] [pool-1-thread-5] Initializing /data/brian/leica-original/050118.lei: [testng] [2024-05-20 01:22:00,263] [pool-1-thread-9] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2024-05-20 01:22:01,262] [pool-1-thread-9] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2024-05-20 01:22:07,014] [pool-1-thread-2] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2024-05-20 01:22:07,635] [pool-1-thread-4] Initializing /data/oliver/o459/o459.lei: [testng] [2024-05-20 01:22:08,018] [pool-1-thread-8] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-05-20 01:22:08,890] [pool-1-thread-1] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] [2024-05-20 01:22:09,611] [pool-1-thread-6] Initializing /data/brian/tropo/tropo.lei: [testng] [2024-05-20 01:22:11,678] [pool-1-thread-6] Initializing /data/clay/leica_stack.lei: [testng] [2024-05-20 01:22:12,352] [pool-1-thread-6] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2024-05-20 01:22:12,686] [pool-1-thread-6] Initializing /data/david/intestine/intestine.lei: [testng] [2024-05-20 01:22:12,881] [pool-1-thread-7] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] [2024-05-20 01:22:14,730] [pool-1-thread-10] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] [2024-05-20 01:22:16,310] [pool-1-thread-10] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2024-05-20 01:22:29,067] [pool-1-thread-1] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-05-20 01:22:33,641] [pool-1-thread-7] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2024-05-20 01:22:33,800] [pool-1-thread-7] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-05-20 01:22:34,762] [pool-1-thread-8] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] [2024-05-20 01:22:34,934] [pool-1-thread-8] Initializing /data/julie/biorad/25-65.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2332, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 3 minutes 30 seconds Finished: SUCCESS