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Started by upstream project "BIOFORMATS-test-repo" build number 384 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/jenkins3806554269745641979.sh + '[' leica = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_60680_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] 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] 12:00:08,589 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 12:00:08,591 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service. [testng] 12:00:08,591 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:00:08,593 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:00:08,593 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 12:00:08,594 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 12:00:08,594 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 12:00:08,594 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:00:08,595 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:00:08,596 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 12:00:08,596 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 12:00:08,596 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 12:00:08,786 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 12:00:08,786 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 12:00:08,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 12:00:08,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 12:00:08,812 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 12:00:08,812 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 12:00:08,812 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 12:00:08,812 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 12:00:08,812 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration. [testng] 12:00:08,813 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point [testng] 12:00:08,813 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 218 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-19 12:00:08,821] [main] java.version = 17.0.2 [testng] 12:00:08,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 12:00:08,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:00:08,884 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-19_12-00-08.log] [testng] 12:00:08,885 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration. [testng] [2025-03-19 12:00:08,905] [main] testng.directory = /data [testng] [2025-03-19 12:00:08,906] [main] testng.configDirectory = /config [testng] [2025-03-19 12:00:09,035] [main] testng.multiplier = 1.0 [testng] [2025-03-19 12:00:09,036] [main] testng.in-memory = false [testng] [2025-03-19 12:00:09,036] [main] testng.allow-missing = false [testng] [2025-03-19 12:00:09,036] [main] user.language = en [testng] [2025-03-19 12:00:09,036] [main] user.country = ${user.country} [testng] [2025-03-19 12:00:09,036] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-19 12:00:49,453] [main] ---------------------------------------- [testng] [2025-03-19 12:00:49,453] [main] Total files: 5651 [testng] [2025-03-19 12:00:49,453] [main] Scan time: 40.417 s (7 ms/file) [testng] [2025-03-19 12:00:49,453] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-19 12:01:38,424] [pool-1-thread-1] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] 12:01:38,425 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 12:01:38,425 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:01:38,426 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-19_12-01-38.log] [testng] 12:01:38,426 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65747d5d - End of configuration. [testng] [2025-03-19 12:01:39,192] [pool-1-thread-12] Initializing /data/constantin/cell6/cell6.lei: [testng] 12:01:39,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 12:01:39,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:01:39,193 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-19_12-01-39.log] [testng] 12:01:39,193 |-INFO in ch.qos.logback.core.sift.SiftProcessor@538cbead - End of configuration. [testng] [2025-03-19 12:01:39,693] [pool-1-thread-11] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] 12:01:39,693 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 12:01:39,693 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:01:39,694 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-19_12-01-39.log] [testng] 12:01:39,694 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72dfc4a4 - End of configuration. [testng] [2025-03-19 12:01:39,757] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] 12:01:39,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 12:01:39,758 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:01:39,759 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-19_12-01-39.log] [testng] 12:01:39,759 |-INFO in ch.qos.logback.core.sift.SiftProcessor@741afe21 - End of configuration. [testng] [2025-03-19 12:01:39,802] [pool-1-thread-9] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] 12:01:39,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 12:01:39,803 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:01:39,803 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-19_12-01-39.log] [testng] 12:01:39,804 |-INFO in ch.qos.logback.core.sift.SiftProcessor@632aac67 - End of configuration. [testng] [2025-03-19 12:01:40,072] [pool-1-thread-8] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] 12:01:40,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 12:01:40,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:01:40,073 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-19_12-01-40.log] [testng] 12:01:40,073 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40251707 - End of configuration. [testng] [2025-03-19 12:01:41,247] [pool-1-thread-7] Initializing /data/brian/tropo/tropo.lei: [testng] 12:01:41,248 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 12:01:41,248 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:01:41,248 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-19_12-01-41.log] [testng] 12:01:41,249 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33513a3e - End of configuration. [testng] [2025-03-19 12:01:41,507] [pool-1-thread-6] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] 12:01:41,507 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 12:01:41,508 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:01:41,508 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-19_12-01-41.log] [testng] 12:01:41,508 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1623033b - End of configuration. [testng] [2025-03-19 12:01:42,532] [pool-1-thread-5] Initializing /data/oliver/o459/o459.lei: [testng] 12:01:42,532 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 12:01:42,532 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:01:42,533 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-19_12-01-42.log] [testng] 12:01:42,534 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b309136 - End of configuration. [testng] [2025-03-19 12:01:42,926] [pool-1-thread-4] Initializing /data/david/megan/megan.lei: [testng] 12:01:42,927 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 12:01:42,927 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:01:42,928 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-19_12-01-42.log] [testng] 12:01:42,928 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66881f48 - End of configuration. [testng] [2025-03-19 12:01:43,378] [pool-1-thread-3] Initializing /data/david/intestine/intestine.lei: [testng] 12:01:43,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 12:01:43,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:01:43,378 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-19_12-01-43.log] [testng] 12:01:43,379 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d52b630 - End of configuration. [testng] [2025-03-19 12:01:43,756] [pool-1-thread-2] Initializing /data/stjude/NIHSSE02-3.lei: [testng] 12:01:43,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 12:01:43,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:01:43,757 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-19_12-01-43.log] [testng] 12:01:43,757 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6080145d - End of configuration. [testng] [2025-03-19 12:01:47,505] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2025-03-19 12:01:47,622] [pool-1-thread-10] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2025-03-19 12:01:51,673] [pool-1-thread-11] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] [2025-03-19 12:02:10,528] [pool-1-thread-7] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] [2025-03-19 12:02:11,619] [pool-1-thread-11] Initializing /data/andrey/10310500/10310500.lei: [testng] [2025-03-19 12:03:48,640] [pool-1-thread-2] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2025-03-19 12:03:57,832] [pool-1-thread-2] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [2025-03-19 12:04:06,166] [pool-1-thread-2] Initializing /data/julie/biorad/25-65.tif: [testng] [2025-03-19 12:04:20,837] [pool-1-thread-2] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2025-03-19 12:06:56,127] [pool-1-thread-9] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2025-03-19 12:08:11,501] [pool-1-thread-2] Initializing /data/julie/c164_1.tif: [testng] [2025-03-19 12:08:23,203] [pool-1-thread-2] Initializing /data/clay/leica_stack.lei: [testng] [2025-03-19 12:08:44,651] [pool-1-thread-2] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] [2025-03-19 12:09:10,297] [pool-1-thread-2] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2025-03-19 12:09:20,947] [pool-1-thread-2] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2025-03-19 12:09:56,993] [pool-1-thread-7] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] [2025-03-19 12:10:39,769] [pool-1-thread-3] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2025-03-19 12:10:59,120] [pool-1-thread-12] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2025-03-19 12:11:04,015] [pool-1-thread-12] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2025-03-19 12:12:08,866] [pool-1-thread-4] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2025-03-19 12:12:12,786] [pool-1-thread-4] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2025-03-19 12:13:46,315] [pool-1-thread-2] Initializing /data/samples/Leica_sample.lei: [testng] [2025-03-19 12:14:02,135] [pool-1-thread-2] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] [2025-03-19 12:14:06,608] [pool-1-thread-2] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2025-03-19 12:16:22,040] [pool-1-thread-4] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] [2025-03-19 12:16:27,320] [pool-1-thread-4] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2025-03-19 12:17:54,415] [pool-1-thread-9] Initializing /data/clay/leica_stack.tif: [testng] [2025-03-19 12:18:01,618] [pool-1-thread-11] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2025-03-19 12:18:04,283] [pool-1-thread-9] Initializing /data/brian/leica-original/050118.lei: [testng] [2025-03-19 12:18:11,072] [pool-1-thread-1] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2025-03-19 12:18:22,805] [pool-1-thread-1] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2025-03-19 12:18:53,416] [pool-1-thread-6] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] 13:56:16,967 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 13:56:16,967 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:56:16,968 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-19_13-56-16.log] [testng] 13:56:16,969 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a1e38ab - 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: 116 minutes 18 seconds Finished: SUCCESS