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Started by upstream project "BIOFORMATS-test-repo" build number 225 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins7463256390392823593.sh + '[' leica = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35430_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings test-automated: [testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 11:08:44,306 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 11:08:44,308 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 11:08:44,308 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:08:44,309 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:08:44,309 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 11:08:44,309 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 11:08:44,310 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 11:08:44,310 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:08:44,310 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:08:44,311 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 11:08:44,311 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:08:44,311 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:08:44,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:08:44,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:08:44,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:08:44,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:08:44,528 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:08:44,529 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:08:44,529 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:08:44,529 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:08:44,529 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 11:08:44,530 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 11:08:44,530 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 220 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-17 11:08:44,538] [main] java.version = 21 [testng] 11:08:44,541 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:08:44,541 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:08:44,580 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-17_11-08-44.log] [testng] 11:08:44,581 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-10-17 11:08:44,583] [main] testng.directory = /data [testng] [2024-10-17 11:08:44,583] [main] testng.configDirectory = /config [testng] [2024-10-17 11:08:44,591] [main] testng.multiplier = 1.0 [testng] [2024-10-17 11:08:44,592] [main] testng.in-memory = false [testng] [2024-10-17 11:08:44,592] [main] testng.allow-missing = false [testng] [2024-10-17 11:08:44,592] [main] user.language = en [testng] [2024-10-17 11:08:44,592] [main] user.country = ${user.country} [testng] [2024-10-17 11:08:44,592] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-17 11:10:28,808] [main] ---------------------------------------- [testng] [2024-10-17 11:10:28,808] [main] Total files: 5651 [testng] [2024-10-17 11:10:28,809] [main] Scan time: 104.215 s (18 ms/file) [testng] [2024-10-17 11:10:28,809] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-17 11:17:56,895] [pool-1-thread-1] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] 11:17:56,896 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 11:17:56,896 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:17:56,897 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-17_11-17-56.log] [testng] 11:17:56,897 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33ba906e - End of configuration. [testng] [2024-10-17 11:18:00,751] [pool-1-thread-12] Initializing /data/clay/leica_stack.tif: [testng] 11:18:00,752 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 11:18:00,752 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:18:00,752 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-17_11-18-00.log] [testng] 11:18:00,753 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2361c467 - End of configuration. [testng] [2024-10-17 11:18:03,880] [pool-1-thread-11] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] 11:18:03,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 11:18:03,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:18:03,881 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-17_11-18-03.log] [testng] 11:18:03,881 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c03a9ed - End of configuration. [testng] [2024-10-17 11:18:07,405] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] 11:18:07,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 11:18:07,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:18:07,406 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-17_11-18-07.log] [testng] 11:18:07,406 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a2f45fd - End of configuration. [testng] [2024-10-17 11:18:07,868] [pool-1-thread-9] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] 11:18:07,868 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 11:18:07,868 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:18:07,869 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-17_11-18-07.log] [testng] 11:18:07,869 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1276c42d - End of configuration. [testng] [2024-10-17 11:18:10,925] [pool-1-thread-8] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] 11:18:10,925 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 11:18:10,925 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:18:10,926 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-17_11-18-10.log] [testng] 11:18:10,927 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b8796eb - End of configuration. [testng] [2024-10-17 11:18:11,339] [pool-1-thread-7] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] 11:18:11,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 11:18:11,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:18:11,341 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-17_11-18-11.log] [testng] 11:18:11,341 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32d00999 - End of configuration. [testng] [2024-10-17 11:18:15,619] [pool-1-thread-6] Initializing /data/brian/leica-original/050118.lei: [testng] 11:18:15,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 11:18:15,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:18:15,620 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-17_11-18-15.log] [testng] 11:18:15,621 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23f469c2 - End of configuration. [testng] [2024-10-17 11:18:22,488] [pool-1-thread-5] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] 11:18:22,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 11:18:22,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:18:22,489 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-17_11-18-22.log] [testng] 11:18:22,489 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3392a533 - End of configuration. [testng] [2024-10-17 11:18:22,605] [pool-1-thread-4] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] 11:18:22,605 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 11:18:22,605 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:18:22,606 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-17_11-18-22.log] [testng] 11:18:22,606 |-INFO in ch.qos.logback.core.sift.SiftProcessor@395430c - End of configuration. [testng] [2024-10-17 11:18:24,877] [pool-1-thread-3] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] 11:18:24,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 11:18:24,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:18:24,878 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-17_11-18-24.log] [testng] 11:18:24,878 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f4ae7 - End of configuration. [testng] [2024-10-17 11:18:26,912] [pool-1-thread-2] Initializing /data/samples/Leica_sample.lei: [testng] 11:18:26,912 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 11:18:26,912 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:18:26,913 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-17_11-18-26.log] [testng] 11:18:26,913 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2096f2dd - End of configuration. [testng] [2024-10-17 11:18:38,978] [pool-1-thread-8] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2024-10-17 11:18:42,697] [pool-1-thread-5] Initializing /data/david/megan/megan.lei: [testng] [2024-10-17 11:18:45,564] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2024-10-17 11:18:49,375] [pool-1-thread-12] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] [2024-10-17 11:18:56,543] [pool-1-thread-10] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2024-10-17 11:19:12,962] [pool-1-thread-2] Initializing /data/julie/biorad/25-65.tif: [testng] [2024-10-17 11:19:28,855] [pool-1-thread-9] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] [2024-10-17 11:19:38,970] [pool-1-thread-1] Initializing /data/david/intestine/intestine.lei: [testng] [2024-10-17 11:19:41,238] [pool-1-thread-2] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2024-10-17 11:30:43,398] [pool-1-thread-12] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-10-17 11:31:57,645] [pool-1-thread-8] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] [2024-10-17 11:32:10,025] [pool-1-thread-8] Initializing /data/brian/tropo/tropo.lei: [testng] [2024-10-17 11:33:58,434] [pool-1-thread-8] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2024-10-17 11:41:48,259] [pool-1-thread-9] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] [2024-10-17 11:42:00,307] [pool-1-thread-9] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2024-10-17 11:42:37,445] [pool-1-thread-9] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] [2024-10-17 11:43:46,127] [pool-1-thread-9] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2024-10-17 11:45:14,845] [pool-1-thread-4] Initializing /data/clay/leica_stack.lei: [testng] [2024-10-17 11:45:26,478] [pool-1-thread-3] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-10-17 11:45:45,938] [pool-1-thread-1] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2024-10-17 11:46:12,010] [pool-1-thread-4] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2024-10-17 11:46:23,149] [pool-1-thread-10] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2024-10-17 11:46:47,847] [pool-1-thread-4] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2024-10-17 11:47:38,354] [pool-1-thread-8] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2024-10-17 11:49:00,719] [pool-1-thread-5] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-10-17 11:49:13,836] [pool-1-thread-5] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-10-17 11:50:47,567] [pool-1-thread-11] Initializing /data/julie/c164_1.tif: [testng] [2024-10-17 11:51:14,875] [pool-1-thread-11] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-10-17 11:51:27,388] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6.lei: [testng] [2024-10-17 11:52:29,041] [pool-1-thread-8] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-10-17 11:57:04,858] [pool-1-thread-6] Initializing /data/oliver/o459/o459.lei: [testng] [2024-10-17 11:58:04,971] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] 13:07:04,614 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 13:07:04,614 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:07:04,615 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-17_13-07-04.log] [testng] 13:07:04,615 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b1a790a - End of configuration. Build was aborted Calling Pipeline was cancelled Finished: ABORTED