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Started by upstream project "BIOFORMATS-test-repo" build number 307 originally caused by: Started by upstream project "Trigger" build number 329 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/jenkins13387550990692279673.sh + '[' leica = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_48551_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] 00:21:59,786 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:21:59,788 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:21:59,788 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:21:59,789 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:21:59,789 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:21:59,789 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:21:59,789 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:21:59,789 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:21:59,790 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:21:59,790 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:21:59,790 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:21:59,790 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:22:00,007 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:22:00,007 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:22:00,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:22:00,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:22:00,040 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:22:00,041 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:22:00,041 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:22:00,041 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:22:00,041 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:22:00,042 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:22:00,042 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 252 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-03 00:22:00,051] [main] java.version = 1.8.0_342 [testng] 00:22:00,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:22:00,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:00,099 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-03_00-22-00.log] [testng] 00:22:00,100 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2025-01-03 00:22:00,102] [main] testng.directory = /data [testng] [2025-01-03 00:22:00,102] [main] testng.configDirectory = /config [testng] [2025-01-03 00:22:00,113] [main] testng.multiplier = 1.0 [testng] [2025-01-03 00:22:00,114] [main] testng.in-memory = false [testng] [2025-01-03 00:22:00,114] [main] testng.allow-missing = false [testng] [2025-01-03 00:22:00,114] [main] user.language = en [testng] [2025-01-03 00:22:00,114] [main] user.country = ${user.country} [testng] [2025-01-03 00:22:00,114] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2025-01-03 00:22:13,279] [main] ---------------------------------------- [testng] [2025-01-03 00:22:13,280] [main] Total files: 5651 [testng] [2025-01-03 00:22:13,280] [main] Scan time: 13.165 s (2 ms/file) [testng] [2025-01-03 00:22:13,280] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-03 00:22:39,108] [pool-1-thread-1] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] 00:22:39,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:22:39,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:39,109 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-03_00-22-39.log] [testng] 00:22:39,110 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72f238bd - End of configuration. [testng] [2025-01-03 00:22:39,173] [pool-1-thread-12] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] 00:22:39,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:22:39,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:39,174 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-03_00-22-39.log] [testng] 00:22:39,174 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d5dc1c4 - End of configuration. [testng] [2025-01-03 00:22:39,419] [pool-1-thread-11] Initializing /data/vytas/4voxels/4voxels.lei: [testng] 00:22:39,419 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:22:39,419 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:39,420 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-03_00-22-39.log] [testng] 00:22:39,421 |-INFO in ch.qos.logback.core.sift.SiftProcessor@217fe5d - End of configuration. [testng] [2025-01-03 00:22:39,631] [pool-1-thread-10] Initializing /data/julie/biorad/25-65.tif: [testng] 00:22:39,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:22:39,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:39,632 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-03_00-22-39.log] [testng] 00:22:39,633 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22d04001 - End of configuration. [testng] [2025-01-03 00:22:40,239] [pool-1-thread-9] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] 00:22:40,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:22:40,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:40,240 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-03_00-22-40.log] [testng] 00:22:40,240 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79bdb69c - End of configuration. [testng] [2025-01-03 00:22:40,412] [pool-1-thread-8] Initializing /data/david/intestine/intestine.lei: [testng] 00:22:40,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:22:40,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:40,413 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-03_00-22-40.log] [testng] 00:22:40,413 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22864719 - End of configuration. [testng] [2025-01-03 00:22:40,603] [pool-1-thread-7] Initializing /data/david/megan/megan.lei: [testng] 00:22:40,604 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:22:40,604 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:40,604 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-03_00-22-40.log] [testng] 00:22:40,605 |-INFO in ch.qos.logback.core.sift.SiftProcessor@148ce9f0 - End of configuration. [testng] [2025-01-03 00:22:40,840] [pool-1-thread-6] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] 00:22:40,840 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:22:40,840 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:40,841 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-03_00-22-40.log] [testng] 00:22:40,842 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f2609f3 - End of configuration. [testng] [2025-01-03 00:22:40,870] [pool-1-thread-5] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] 00:22:40,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:22:40,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:40,871 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-03_00-22-40.log] [testng] 00:22:40,871 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56b5aa67 - End of configuration. [testng] [2025-01-03 00:22:41,192] [pool-1-thread-4] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] 00:22:41,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:22:41,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:41,192 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-03_00-22-41.log] [testng] 00:22:41,193 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bbb6919 - End of configuration. [testng] [2025-01-03 00:22:41,444] [pool-1-thread-3] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] 00:22:41,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:22:41,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:41,445 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-03_00-22-41.log] [testng] 00:22:41,446 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9350cb5 - End of configuration. [testng] [2025-01-03 00:22:41,931] [pool-1-thread-2] Initializing /data/oliver/o459/o459.lei: [testng] 00:22:41,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:22:41,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:41,932 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-03_00-22-41.log] [testng] 00:22:41,932 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21dc7252 - End of configuration. [testng] [2025-01-03 00:22:45,576] [pool-1-thread-1] Initializing /data/samples/Leica_sample.lei: [testng] [2025-01-03 00:22:46,275] [pool-1-thread-6] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2025-01-03 00:22:51,509] [pool-1-thread-10] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] [2025-01-03 00:22:55,952] [pool-1-thread-3] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] [2025-01-03 00:22:56,458] [pool-1-thread-1] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] [2025-01-03 00:22:58,301] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [2025-01-03 00:23:01,523] [pool-1-thread-3] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2025-01-03 00:23:06,767] [pool-1-thread-1] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2025-01-03 00:23:15,404] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2025-01-03 00:23:17,895] [pool-1-thread-1] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2025-01-03 00:23:20,421] [pool-1-thread-1] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2025-01-03 00:24:45,542] [pool-1-thread-5] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2025-01-03 00:24:47,182] [pool-1-thread-5] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2025-01-03 00:25:27,232] [pool-1-thread-9] Initializing /data/clay/leica_stack.lei: [testng] [2025-01-03 00:25:41,564] [pool-1-thread-9] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2025-01-03 00:25:45,482] [pool-1-thread-9] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2025-01-03 00:26:52,724] [pool-1-thread-10] Initializing /data/brian/tropo/tropo.lei: [testng] [2025-01-03 00:27:21,573] [pool-1-thread-10] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2025-01-03 00:27:38,067] [pool-1-thread-5] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] [2025-01-03 00:27:48,444] [pool-1-thread-8] Initializing /data/clay/leica_stack.tif: [testng] [2025-01-03 00:27:48,890] [pool-1-thread-4] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2025-01-03 00:27:50,311] [pool-1-thread-4] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2025-01-03 00:27:51,616] [pool-1-thread-8] Initializing /data/julie/c164_1.tif: [testng] [2025-01-03 00:27:59,510] [pool-1-thread-8] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2025-01-03 00:28:05,220] [pool-1-thread-9] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2025-01-03 00:28:14,343] [pool-1-thread-9] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2025-01-03 00:28:16,770] [pool-1-thread-10] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2025-01-03 00:28:24,639] [pool-1-thread-7] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2025-01-03 00:28:30,976] [pool-1-thread-1] Initializing /data/andrey/10310500/10310500.lei: [testng] [2025-01-03 00:28:43,602] [pool-1-thread-12] Initializing /data/brian/leica-original/050118.lei: [testng] [2025-01-03 00:29:42,953] [pool-1-thread-5] Initializing /data/constantin/cell6/cell6.lei: [testng] [2025-01-03 00:29:49,608] [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 9 seconds Finished: SUCCESS