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Started by upstream project "BIOFORMATS-test-repo" build number 379 originally caused by: Started by upstream project "Trigger" build number 401 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/jenkins14920978485113131362.sh + '[' leica = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_59895_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] 00:24:08,106 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:24:08,108 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - No custom configurators were discovered as a service. [testng] 00:24:08,108 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:24:08,109 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:24:08,109 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:24:08,109 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:24:08,110 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:24:08,110 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:24:08,110 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:24:08,111 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:24:08,111 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:24:08,111 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:24:08,269 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:24:08,269 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:24:08,290 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:24:08,290 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:24:08,295 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:24:08,295 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:24:08,295 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:24:08,295 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:24:08,295 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@65c7a252 - End of configuration. [testng] 00:24:08,296 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@38cee291 - Registering current configuration as safe fallback point [testng] 00:24:08,296 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 186 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-15 00:24:08,305] [main] java.version = 11.0.16 [testng] 00:24:08,307 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:24:08,307 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:08,347 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-15_00-24-08.log] [testng] 00:24:08,349 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13d73f29 - End of configuration. [testng] [2025-03-15 00:24:08,351] [main] testng.directory = /data [testng] [2025-03-15 00:24:08,351] [main] testng.configDirectory = /config [testng] [2025-03-15 00:24:08,360] [main] testng.multiplier = 1.0 [testng] [2025-03-15 00:24:08,361] [main] testng.in-memory = false [testng] [2025-03-15 00:24:08,361] [main] testng.allow-missing = false [testng] [2025-03-15 00:24:08,361] [main] user.language = en [testng] [2025-03-15 00:24:08,361] [main] user.country = ${user.country} [testng] [2025-03-15 00:24:08,361] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-15 00:24:29,857] [main] ---------------------------------------- [testng] [2025-03-15 00:24:29,857] [main] Total files: 5651 [testng] [2025-03-15 00:24:29,858] [main] Scan time: 21.495 s (3 ms/file) [testng] [2025-03-15 00:24:29,858] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-15 00:26:38,607] [pool-1-thread-1] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] 00:26:38,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:26:38,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:38,609 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-15_00-26-38.log] [testng] 00:26:38,610 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c3527bb - End of configuration. [testng] [2025-03-15 00:26:40,048] [pool-1-thread-12] Initializing /data/brian/tropo/tropo.lei: [testng] 00:26:40,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:26:40,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:40,049 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-15_00-26-40.log] [testng] 00:26:40,049 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2dc8ee83 - End of configuration. [testng] [2025-03-15 00:26:42,437] [pool-1-thread-11] Initializing /data/simon/Leica demo/test/test.lei: [testng] 00:26:42,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:26:42,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:42,438 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-15_00-26-42.log] [testng] 00:26:42,439 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a01c786 - End of configuration. [testng] [2025-03-15 00:26:45,561] [pool-1-thread-10] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] 00:26:45,562 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:26:45,562 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:45,563 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-15_00-26-45.log] [testng] 00:26:45,563 |-INFO in ch.qos.logback.core.sift.SiftProcessor@271c98c9 - End of configuration. [testng] [2025-03-15 00:26:48,389] [pool-1-thread-9] Initializing /data/julie/biorad/25-65.tif: [testng] 00:26:48,389 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:26:48,389 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:48,390 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-15_00-26-48.log] [testng] 00:26:48,390 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bbe623 - End of configuration. [testng] [2025-03-15 00:26:50,087] [pool-1-thread-8] Initializing /data/constantin/cell6/cell6.lei: [testng] 00:26:50,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:26:50,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:50,088 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-15_00-26-50.log] [testng] 00:26:50,088 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48e62e70 - End of configuration. [testng] [2025-03-15 00:26:51,570] [pool-1-thread-7] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] 00:26:51,570 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:26:51,570 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:51,570 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-15_00-26-51.log] [testng] 00:26:51,571 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a0974eb - End of configuration. [testng] [2025-03-15 00:26:52,977] [pool-1-thread-6] Initializing /data/samples/Leica_sample.lei: [testng] 00:26:52,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:26:52,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:52,977 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-15_00-26-52.log] [testng] 00:26:52,978 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20d3afa3 - End of configuration. [testng] [2025-03-15 00:26:54,181] [pool-1-thread-5] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] 00:26:54,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:26:54,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:54,181 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-15_00-26-54.log] [testng] 00:26:54,182 |-INFO in ch.qos.logback.core.sift.SiftProcessor@966d13b - End of configuration. [testng] [2025-03-15 00:26:54,449] [pool-1-thread-4] Initializing /data/clay/leica_stack.tif: [testng] 00:26:54,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:26:54,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:54,449 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-15_00-26-54.log] [testng] 00:26:54,450 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49012c5d - End of configuration. [testng] [2025-03-15 00:26:56,545] [pool-1-thread-3] Initializing /data/vytas/4voxels/4voxels.lei: [testng] 00:26:56,546 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:26:56,546 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:56,546 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-15_00-26-56.log] [testng] 00:26:56,547 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46150b72 - End of configuration. [testng] [2025-03-15 00:26:57,967] [pool-1-thread-2] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] 00:26:57,967 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:26:57,967 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:57,967 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-15_00-26-57.log] [testng] 00:26:57,968 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64983ff7 - End of configuration. [testng] [2025-03-15 00:27:08,380] [pool-1-thread-5] Initializing /data/julie/c164_1.tif: [testng] [2025-03-15 00:27:19,275] [pool-1-thread-4] Initializing /data/andrey/10310500/10310500.lei: [testng] [2025-03-15 00:27:29,055] [pool-1-thread-9] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2025-03-15 00:27:34,705] [pool-1-thread-6] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] [2025-03-15 00:27:38,358] [pool-1-thread-5] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] [2025-03-15 00:27:46,072] [pool-1-thread-1] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] [2025-03-15 00:27:52,218] [pool-1-thread-1] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2025-03-15 00:28:04,305] [pool-1-thread-12] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2025-03-15 00:28:14,764] [pool-1-thread-12] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2025-03-15 00:28:33,529] [pool-1-thread-6] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2025-03-15 00:28:42,682] [pool-1-thread-12] Initializing /data/oliver/o459/o459.lei: [testng] [2025-03-15 00:30:55,078] [pool-1-thread-1] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] [2025-03-15 00:31:02,101] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2025-03-15 00:31:08,078] [pool-1-thread-1] Initializing /data/david/intestine/intestine.lei: [testng] [2025-03-15 00:34:52,035] [pool-1-thread-9] Initializing /data/brian/leica-original/050118.lei: [testng] [2025-03-15 00:35:11,393] [pool-1-thread-7] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2025-03-15 00:40:23,346] [pool-1-thread-8] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] [2025-03-15 00:40:24,325] [pool-1-thread-7] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2025-03-15 00:40:28,237] [pool-1-thread-7] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2025-03-15 00:40:39,376] [pool-1-thread-2] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2025-03-15 00:40:45,776] [pool-1-thread-8] Initializing /data/clay/leica_stack.lei: [testng] [2025-03-15 00:40:47,758] [pool-1-thread-7] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2025-03-15 00:40:51,742] [pool-1-thread-5] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2025-03-15 00:40:59,882] [pool-1-thread-7] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] [2025-03-15 00:41:12,599] [pool-1-thread-8] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2025-03-15 00:41:16,285] [pool-1-thread-8] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2025-03-15 00:42:48,210] [pool-1-thread-1] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2025-03-15 00:44:36,280] [pool-1-thread-11] Initializing /data/david/megan/megan.lei: [testng] [2025-03-15 00:47:29,007] [pool-1-thread-6] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2025-03-15 00:49:29,610] [pool-1-thread-1] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2025-03-15 00:49:38,348] [pool-1-thread-8] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2025-03-15 00:49:40,658] [pool-1-thread-4] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] 04:40:39,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:40:39,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:40:39,497 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-15_04-40-39.log] [testng] 04:40:39,497 |-INFO in ch.qos.logback.core.sift.SiftProcessor@294a12b5 - 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: 256 minutes 34 seconds Finished: SUCCESS