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Started by upstream project "BIOFORMATS-test-repo" build number 221 originally caused by: Started by upstream project "Trigger" build number 248 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/jenkins13713557255992965544.sh + '[' leica = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35023_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 [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] 1 warning test-automated: [testng] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 01:30:36,197 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:30:36,198 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 01:30:36,198 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:30:36,199 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:30:36,199 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:30:36,200 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:30:36,200 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:30:36,200 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:30:36,200 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:30:36,201 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:30:36,201 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:30:36,201 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:30:36,358 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:30:36,358 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:30:36,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:30:36,379 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:30:36,384 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:30:36,384 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:30:36,384 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:30:36,384 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:30:36,384 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 01:30:36,385 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 01:30:36,385 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 185 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-15 01:30:36,393] [main] java.version = 11.0.16 [testng] 01:30:36,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:30:36,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:30:36,436 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-15_01-30-36.log] [testng] 01:30:36,437 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-15 01:30:36,439] [main] testng.directory = /data [testng] [2024-10-15 01:30:36,439] [main] testng.configDirectory = /config [testng] [2024-10-15 01:30:36,449] [main] testng.multiplier = 1.0 [testng] [2024-10-15 01:30:36,450] [main] testng.in-memory = false [testng] [2024-10-15 01:30:36,450] [main] testng.allow-missing = false [testng] [2024-10-15 01:30:36,450] [main] user.language = en [testng] [2024-10-15 01:30:36,450] [main] user.country = ${user.country} [testng] [2024-10-15 01:30:36,450] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-15 01:33:50,738] [main] ---------------------------------------- [testng] [2024-10-15 01:33:50,739] [main] Total files: 5651 [testng] [2024-10-15 01:33:50,739] [main] Scan time: 194.288 s (34 ms/file) [testng] [2024-10-15 01:33:50,739] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-15 01:37:56,273] [pool-1-thread-1] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] 01:37:56,274 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:37:56,274 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:56,276 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-15_01-37-56.log] [testng] 01:37:56,276 |-INFO in ch.qos.logback.core.sift.SiftProcessor@dea701c - End of configuration. [testng] [2024-10-15 01:38:00,531] [pool-1-thread-12] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] 01:38:00,531 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:38:00,532 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:00,532 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-15_01-38-00.log] [testng] 01:38:00,533 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56a06251 - End of configuration. [testng] [2024-10-15 01:38:04,466] [pool-1-thread-11] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] 01:38:04,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:38:04,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:04,467 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-15_01-38-04.log] [testng] 01:38:04,467 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48e62e70 - End of configuration. [testng] [2024-10-15 01:38:07,206] [pool-1-thread-10] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] 01:38:07,206 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:38:07,206 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:07,207 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-15_01-38-07.log] [testng] 01:38:07,207 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3253f0a3 - End of configuration. [testng] [2024-10-15 01:38:09,815] [pool-1-thread-9] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] 01:38:09,815 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:38:09,815 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:09,816 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-15_01-38-09.log] [testng] 01:38:09,816 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43cbf40f - End of configuration. [testng] [2024-10-15 01:38:10,193] [pool-1-thread-8] Initializing /data/constantin/cell6/Logo.jpg: [testng] 01:38:10,193 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:38:10,193 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:10,194 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-15_01-38-10.log] [testng] 01:38:10,194 |-INFO in ch.qos.logback.core.sift.SiftProcessor@cb66b22 - End of configuration. [testng] [2024-10-15 01:38:10,589] [pool-1-thread-7] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] 01:38:10,589 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:38:10,589 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:10,590 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-15_01-38-10.log] [testng] 01:38:10,590 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ec8fc2b - End of configuration. [testng] [2024-10-15 01:38:15,427] [pool-1-thread-6] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] 01:38:15,428 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:38:15,428 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:15,428 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-15_01-38-15.log] [testng] 01:38:15,428 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48af19f9 - End of configuration. [testng] [2024-10-15 01:38:16,648] [pool-1-thread-5] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] 01:38:16,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:38:16,649 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:16,649 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-15_01-38-16.log] [testng] 01:38:16,650 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b320871 - End of configuration. [testng] [2024-10-15 01:38:18,060] [pool-1-thread-4] Initializing /data/brian/leica-original/050118.lei: [testng] 01:38:18,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:38:18,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:18,061 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-15_01-38-18.log] [testng] 01:38:18,061 |-INFO in ch.qos.logback.core.sift.SiftProcessor@966d13b - End of configuration. [testng] [2024-10-15 01:38:23,080] [pool-1-thread-3] Initializing /data/oliver/o459/o459.lei: [testng] 01:38:23,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:38:23,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:23,081 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-15_01-38-23.log] [testng] 01:38:23,081 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49012c5d - End of configuration. [testng] [2024-10-15 01:38:24,770] [pool-1-thread-2] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] 01:38:24,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:38:24,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:24,771 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-15_01-38-24.log] [testng] 01:38:24,771 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3204ebcf - End of configuration. [testng] [2024-10-15 01:38:34,909] [pool-1-thread-8] Initializing /data/constantin/cell6/cell6.lei: [testng] [2024-10-15 01:38:37,198] [pool-1-thread-2] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2024-10-15 01:38:40,499] [pool-1-thread-9] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-10-15 01:39:07,091] [pool-1-thread-6] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-10-15 01:44:55,265] [pool-1-thread-5] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-10-15 01:46:35,291] [pool-1-thread-11] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2024-10-15 01:46:51,677] [pool-1-thread-11] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] [2024-10-15 01:47:38,117] [pool-1-thread-11] Initializing /data/brian/tropo/tropo.lei: [testng] [2024-10-15 01:48:26,728] [pool-1-thread-11] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] [2024-10-15 01:48:31,888] [pool-1-thread-11] Initializing /data/julie/biorad/25-65.tif: [testng] [2024-10-15 01:48:46,902] [pool-1-thread-11] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2024-10-15 01:49:00,363] [pool-1-thread-11] Initializing /data/clay/leica_stack.lei: [testng] [2024-10-15 01:49:31,422] [pool-1-thread-11] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] [2024-10-15 01:49:37,534] [pool-1-thread-11] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2024-10-15 01:49:53,289] [pool-1-thread-12] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [2024-10-15 01:49:59,844] [pool-1-thread-12] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] [2024-10-15 01:52:21,045] [pool-1-thread-10] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2024-10-15 01:52:35,424] [pool-1-thread-8] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2024-10-15 01:53:03,125] [pool-1-thread-2] Initializing /data/clay/leica_stack.tif: [testng] [2024-10-15 01:53:21,751] [pool-1-thread-2] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-10-15 01:58:18,413] [pool-1-thread-12] Initializing /data/david/megan/megan.lei: [testng] [2024-10-15 01:59:52,591] [pool-1-thread-1] Initializing /data/samples/Leica_sample.lei: [testng] [2024-10-15 02:00:04,788] [pool-1-thread-10] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2024-10-15 02:00:29,194] [pool-1-thread-1] Initializing /data/julie/c164_1.tif: [testng] [2024-10-15 02:00:32,490] [pool-1-thread-4] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] [2024-10-15 02:00:51,912] [pool-1-thread-1] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2024-10-15 02:01:34,872] [pool-1-thread-4] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] [2024-10-15 02:01:41,963] [pool-1-thread-4] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2024-10-15 02:02:19,148] [pool-1-thread-2] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2024-10-15 02:02:24,921] [pool-1-thread-2] Initializing /data/david/intestine/intestine.lei: [testng] [2024-10-15 02:03:21,589] [pool-1-thread-10] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-10-15 02:03:32,014] [pool-1-thread-10] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] 05:19:56,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:19:56,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:19:56,522 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-15_05-19-56.log] [testng] 05:19:56,522 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19542115 - 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: 229 minutes 24 seconds Finished: SUCCESS