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Started by upstream project "BIOFORMATS-test-repo" build number 314 originally caused by: Started by upstream project "Trigger" build number 336 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/jenkins657830418349726935.sh + '[' leica = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_49706_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 test-automated: [testng] File leak detector installed [testng] 01:14:19,643 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:14:19,645 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 01:14:19,645 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:14:19,646 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:14:19,646 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:14:19,646 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:14:19,647 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:14:19,647 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:14:19,647 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:14:19,648 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:14:19,648 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:14:19,648 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:14:19,882 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:14:19,882 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:14:19,910 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:14:19,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:14:19,919 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:14:19,919 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:14:19,920 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:14:19,920 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:14:19,920 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 01:14:19,921 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 01:14:19,921 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 274 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-10 01:14:19,931] [main] java.version = 1.8.0_342 [testng] 01:14:19,934 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:14:19,934 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:19,981 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-10_01-14-19.log] [testng] 01:14:19,982 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2025-01-10 01:14:19,984] [main] testng.directory = /data [testng] [2025-01-10 01:14:19,984] [main] testng.configDirectory = /config [testng] [2025-01-10 01:14:19,997] [main] testng.multiplier = 1.0 [testng] [2025-01-10 01:14:19,997] [main] testng.in-memory = false [testng] [2025-01-10 01:14:19,997] [main] testng.allow-missing = false [testng] [2025-01-10 01:14:19,997] [main] user.language = en [testng] [2025-01-10 01:14:19,997] [main] user.country = ${user.country} [testng] [2025-01-10 01:14:19,997] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2025-01-10 01:14:34,448] [main] ---------------------------------------- [testng] [2025-01-10 01:14:34,448] [main] Total files: 5651 [testng] [2025-01-10 01:14:34,448] [main] Scan time: 14.451 s (2 ms/file) [testng] [2025-01-10 01:14:34,449] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-10 01:15:05,087] [pool-1-thread-1] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] 01:15:05,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:15:05,088 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:05,089 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-10_01-15-05.log] [testng] 01:15:05,089 |-INFO in ch.qos.logback.core.sift.SiftProcessor@784abbe8 - End of configuration. [testng] [2025-01-10 01:15:05,159] [pool-1-thread-12] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] 01:15:05,159 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:15:05,159 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:05,160 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-10_01-15-05.log] [testng] 01:15:05,160 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e8d069b - End of configuration. [testng] [2025-01-10 01:15:05,940] [pool-1-thread-11] Initializing /data/vytas/4voxels/4voxels.lei: [testng] 01:15:05,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:15:05,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:05,941 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-10_01-15-05.log] [testng] 01:15:05,941 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27c364cc - End of configuration. [testng] [2025-01-10 01:15:06,779] [pool-1-thread-10] Initializing /data/julie/biorad/25-65.tif: [testng] 01:15:06,780 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:15:06,780 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:06,780 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-10_01-15-06.log] [testng] 01:15:06,781 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63212c5d - End of configuration. [testng] [2025-01-10 01:15:07,319] [pool-1-thread-9] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] 01:15:07,320 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:15:07,320 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:07,320 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-10_01-15-07.log] [testng] 01:15:07,320 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e6a5021 - End of configuration. [testng] [2025-01-10 01:15:09,095] [pool-1-thread-8] Initializing /data/david/intestine/intestine.lei: [testng] 01:15:09,095 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:15:09,095 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:09,096 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-10_01-15-09.log] [testng] 01:15:09,096 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22864719 - End of configuration. [testng] [2025-01-10 01:15:09,814] [pool-1-thread-7] Initializing /data/david/megan/megan.lei: [testng] 01:15:09,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:15:09,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:09,814 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-10_01-15-09.log] [testng] 01:15:09,815 |-INFO in ch.qos.logback.core.sift.SiftProcessor@225c7073 - End of configuration. [testng] [2025-01-10 01:15:10,598] [pool-1-thread-6] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] 01:15:10,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:15:10,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:10,599 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-10_01-15-10.log] [testng] 01:15:10,599 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9f1715d - End of configuration. [testng] [2025-01-10 01:15:10,644] [pool-1-thread-5] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] 01:15:10,644 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:15:10,644 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:10,645 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-10_01-15-10.log] [testng] 01:15:10,645 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d43f40f - End of configuration. [testng] [2025-01-10 01:15:10,908] [pool-1-thread-4] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] 01:15:10,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:15:10,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:10,908 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-10_01-15-10.log] [testng] 01:15:10,909 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57ecc1b3 - End of configuration. [testng] [2025-01-10 01:15:11,182] [pool-1-thread-3] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] 01:15:11,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:15:11,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:11,183 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-10_01-15-11.log] [testng] 01:15:11,183 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75b06c82 - End of configuration. [testng] [2025-01-10 01:15:11,377] [pool-1-thread-2] Initializing /data/oliver/o459/o459.lei: [testng] 01:15:11,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:15:11,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:11,379 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-10_01-15-11.log] [testng] 01:15:11,380 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e03cbd8 - End of configuration. [testng] [2025-01-10 01:15:15,698] [pool-1-thread-1] Initializing /data/samples/Leica_sample.lei: [testng] [2025-01-10 01:15:16,296] [pool-1-thread-6] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2025-01-10 01:15:24,357] [pool-1-thread-10] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] [2025-01-10 01:15:29,238] [pool-1-thread-3] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] [2025-01-10 01:15:30,496] [pool-1-thread-1] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] [2025-01-10 01:15:32,507] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [2025-01-10 01:15:35,906] [pool-1-thread-3] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2025-01-10 01:15:45,472] [pool-1-thread-1] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2025-01-10 01:15:51,950] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2025-01-10 01:15:54,730] [pool-1-thread-1] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2025-01-10 01:15:58,474] [pool-1-thread-1] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2025-01-10 01:17:27,852] [pool-1-thread-5] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2025-01-10 01:17:29,696] [pool-1-thread-5] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2025-01-10 01:18:10,529] [pool-1-thread-9] Initializing /data/clay/leica_stack.lei: [testng] [2025-01-10 01:18:29,497] [pool-1-thread-9] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2025-01-10 01:18:31,710] [pool-1-thread-9] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2025-01-10 01:19:52,194] [pool-1-thread-10] Initializing /data/brian/tropo/tropo.lei: [testng] [2025-01-10 01:20:21,804] [pool-1-thread-10] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2025-01-10 01:20:37,847] [pool-1-thread-5] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] [2025-01-10 01:20:44,992] [pool-1-thread-8] Initializing /data/clay/leica_stack.tif: [testng] [2025-01-10 01:20:46,185] [pool-1-thread-4] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2025-01-10 01:20:47,756] [pool-1-thread-4] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2025-01-10 01:20:48,664] [pool-1-thread-8] Initializing /data/julie/c164_1.tif: [testng] [2025-01-10 01:20:55,909] [pool-1-thread-8] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2025-01-10 01:21:01,131] [pool-1-thread-9] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2025-01-10 01:21:07,761] [pool-1-thread-9] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2025-01-10 01:21:10,865] [pool-1-thread-10] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2025-01-10 01:21:19,120] [pool-1-thread-7] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2025-01-10 01:21:26,764] [pool-1-thread-1] Initializing /data/andrey/10310500/10310500.lei: [testng] [2025-01-10 01:21:40,480] [pool-1-thread-12] Initializing /data/brian/leica-original/050118.lei: [testng] [2025-01-10 01:22:43,600] [pool-1-thread-5] Initializing /data/constantin/cell6/cell6.lei: [testng] [2025-01-10 01:22:48,395] [pool-1-thread-3] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2332, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 31 minutes 16 seconds Finished: SUCCESS