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Started by upstream project "BIOFORMATS-test-repo" build number 293 originally caused by: Started by upstream project "Trigger" build number 312 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/jenkins11413577029662029691.sh + '[' leica = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_46240_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] 00:22:48,696 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:22:48,698 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 00:22:48,698 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:22:48,698 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:22:48,699 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:22:48,699 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:22:48,700 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:22:48,700 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:22:48,700 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:22:48,701 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:22:48,701 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:22:48,701 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:22:48,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:22:48,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:22:48,886 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:22:48,886 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:22:48,892 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:22:48,892 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:22:48,892 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:22:48,892 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:22:48,892 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 00:22:48,893 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 00:22:48,893 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 193 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-17 00:22:48,901] [main] java.version = 11.0.16 [testng] 00:22:48,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:22:48,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:48,946 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-17_00-22-48.log] [testng] 00:22:48,947 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-12-17 00:22:48,949] [main] testng.directory = /data [testng] [2024-12-17 00:22:48,949] [main] testng.configDirectory = /config [testng] [2024-12-17 00:22:48,958] [main] testng.multiplier = 1.0 [testng] [2024-12-17 00:22:48,960] [main] testng.in-memory = false [testng] [2024-12-17 00:22:48,960] [main] testng.allow-missing = false [testng] [2024-12-17 00:22:48,960] [main] user.language = en [testng] [2024-12-17 00:22:48,960] [main] user.country = ${user.country} [testng] [2024-12-17 00:22:48,960] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-17 00:27:34,320] [main] ---------------------------------------- [testng] [2024-12-17 00:27:34,321] [main] Total files: 5651 [testng] [2024-12-17 00:27:34,321] [main] Scan time: 285.36 s (50 ms/file) [testng] [2024-12-17 00:27:34,321] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-17 00:32:38,527] [pool-1-thread-1] Initializing /data/constantin/cell6/Logo.jpg: [testng] 00:32:38,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:32:38,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:38,529 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-17_00-32-38.log] [testng] 00:32:38,530 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41c1a691 - End of configuration. [testng] [2024-12-17 00:32:39,172] [pool-1-thread-12] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] 00:32:39,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:32:39,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:39,174 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-17_00-32-39.log] [testng] 00:32:39,174 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7bee811b - End of configuration. [testng] [2024-12-17 00:32:39,617] [pool-1-thread-11] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] 00:32:39,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:32:39,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:39,618 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-17_00-32-39.log] [testng] 00:32:39,618 |-INFO in ch.qos.logback.core.sift.SiftProcessor@382580ac - End of configuration. [testng] [2024-12-17 00:32:45,714] [pool-1-thread-10] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] 00:32:45,715 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:32:45,715 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:45,715 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-17_00-32-45.log] [testng] 00:32:45,716 |-INFO in ch.qos.logback.core.sift.SiftProcessor@779bd46a - End of configuration. [testng] [2024-12-17 00:32:48,166] [pool-1-thread-9] Initializing /data/julie/biorad/25-65.tif: [testng] 00:32:48,166 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:32:48,166 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:48,166 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-17_00-32-48.log] [testng] 00:32:48,167 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75020664 - End of configuration. [testng] [2024-12-17 00:32:50,828] [pool-1-thread-8] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] 00:32:50,828 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:32:50,828 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:50,829 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-17_00-32-50.log] [testng] 00:32:50,829 |-INFO in ch.qos.logback.core.sift.SiftProcessor@736f5791 - End of configuration. [testng] [2024-12-17 00:32:51,265] [pool-1-thread-7] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] 00:32:51,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:32:51,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:51,266 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-17_00-32-51.log] [testng] 00:32:51,267 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5467b207 - End of configuration. [testng] [2024-12-17 00:32:54,841] [pool-1-thread-6] Initializing /data/simon/Leica demo/test/test.lei: [testng] 00:32:54,841 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:32:54,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:54,842 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-17_00-32-54.log] [testng] 00:32:54,842 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a2a91e4 - End of configuration. [testng] [2024-12-17 00:32:57,317] [pool-1-thread-5] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] 00:32:57,317 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:32:57,318 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:57,318 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-17_00-32-57.log] [testng] 00:32:57,318 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c4a44c1 - End of configuration. [testng] [2024-12-17 00:33:14,960] [pool-1-thread-4] Initializing /data/david/megan/megan.lei: [testng] 00:33:14,960 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:33:14,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:14,961 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-17_00-33-14.log] [testng] 00:33:14,961 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d13d99 - End of configuration. [testng] [2024-12-17 00:33:20,865] [pool-1-thread-3] Initializing /data/brian/leica-original/050118.lei: [testng] 00:33:20,865 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:33:20,865 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:20,866 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-17_00-33-20.log] [testng] 00:33:20,866 |-INFO in ch.qos.logback.core.sift.SiftProcessor@756fe5d0 - End of configuration. [testng] [2024-12-17 00:33:32,568] [pool-1-thread-2] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] 00:33:32,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:33:32,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:32,569 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-17_00-33-32.log] [testng] 00:33:32,569 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4173fd7b - End of configuration. [testng] [2024-12-17 00:33:50,870] [pool-1-thread-8] Initializing /data/constantin/cell6/cell6.lei: [testng] [2024-12-17 00:34:00,193] [pool-1-thread-12] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2024-12-17 00:34:00,497] [pool-1-thread-1] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-12-17 00:34:09,320] [pool-1-thread-12] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2024-12-17 00:34:14,795] [pool-1-thread-9] Initializing /data/julie/c164_1.tif: [testng] [2024-12-17 00:34:19,667] [pool-1-thread-10] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2024-12-17 00:34:34,598] [pool-1-thread-9] Initializing /data/clay/leica_stack.tif: [testng] [2024-12-17 00:34:42,335] [pool-1-thread-9] Initializing /data/david/intestine/intestine.lei: [testng] [2024-12-17 00:38:48,954] [pool-1-thread-7] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-12-17 00:39:52,059] [pool-1-thread-1] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2024-12-17 00:45:40,002] [pool-1-thread-11] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] [2024-12-17 00:45:53,462] [pool-1-thread-8] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2024-12-17 00:45:57,396] [pool-1-thread-5] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] [2024-12-17 00:46:40,076] [pool-1-thread-9] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2024-12-17 00:47:15,503] [pool-1-thread-5] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] [2024-12-17 00:47:29,935] [pool-1-thread-5] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] [2024-12-17 00:48:23,633] [pool-1-thread-4] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-12-17 00:48:32,042] [pool-1-thread-5] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2024-12-17 00:49:40,376] [pool-1-thread-2] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2024-12-17 00:50:28,482] [pool-1-thread-2] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2024-12-17 00:52:26,929] [pool-1-thread-5] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2024-12-17 00:52:31,748] [pool-1-thread-5] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2024-12-17 00:52:52,802] [pool-1-thread-6] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] [2024-12-17 00:54:17,728] [pool-1-thread-8] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-12-17 00:54:26,204] [pool-1-thread-12] Initializing /data/brian/tropo/tropo.lei: [testng] [2024-12-17 00:54:34,673] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [2024-12-17 00:54:41,093] [pool-1-thread-3] Initializing /data/clay/leica_stack.lei: [testng] [2024-12-17 00:55:13,774] [pool-1-thread-11] Initializing /data/samples/Leica_sample.lei: [testng] [2024-12-17 00:55:27,908] [pool-1-thread-3] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-12-17 00:55:31,043] [pool-1-thread-12] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2024-12-17 00:55:34,627] [pool-1-thread-3] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2024-12-17 00:55:40,115] [pool-1-thread-11] Initializing /data/oliver/o459/o459.lei: [testng] 05:00:45,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 05:00:45,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:00:45,117 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-17_05-00-45.log] [testng] 05:00:45,117 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77c4a86 - End of configuration. [testng] 05:08:48,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:08:48,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:48,906 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-17_05-08-48.log] [testng] 05:08:48,906 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79982bcc - 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: 286 minutes 3 seconds Finished: SUCCESS