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Started by upstream project "BIOFORMATS-test-repo" build number 306 originally caused by: Started by upstream project "Trigger" build number 328 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/jenkins6256491283060852446.sh + '[' leica = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_48386_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 00:35:25,240 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:35:25,241 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 00:35:25,241 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:35:25,242 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:35:25,243 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:35:25,243 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:35:25,243 |-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] 00:35:25,243 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:35:25,244 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:35:25,244 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:35:25,245 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:35:25,245 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:35:25,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:35:25,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:35:25,470 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:35:25,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:35:25,477 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:35:25,477 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:35:25,477 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:35:25,477 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:35:25,477 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 00:35:25,478 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 00:35:25,478 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 234 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-02 00:35:25,487] [main] java.version = 21 [testng] 00:35:25,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:35:25,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:25,530 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-02_00-35-25.log] [testng] 00:35:25,531 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2025-01-02 00:35:25,532] [main] testng.directory = /data [testng] [2025-01-02 00:35:25,532] [main] testng.configDirectory = /config [testng] [2025-01-02 00:35:25,541] [main] testng.multiplier = 1.0 [testng] [2025-01-02 00:35:25,542] [main] testng.in-memory = false [testng] [2025-01-02 00:35:25,542] [main] testng.allow-missing = false [testng] [2025-01-02 00:35:25,542] [main] user.language = en [testng] [2025-01-02 00:35:25,542] [main] user.country = ${user.country} [testng] [2025-01-02 00:35:25,542] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-01-02 00:35:39,654] [main] ---------------------------------------- [testng] [2025-01-02 00:35:39,654] [main] Total files: 5651 [testng] [2025-01-02 00:35:39,654] [main] Scan time: 14.111 s (2 ms/file) [testng] [2025-01-02 00:35:39,655] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-02 00:36:04,332] [pool-1-thread-1] Initializing /data/simon/Leica demo/test/test.lei: [testng] 00:36:04,332 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:36:04,332 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:04,333 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-02_00-36-04.log] [testng] 00:36:04,334 |-INFO in ch.qos.logback.core.sift.SiftProcessor@472cffc2 - End of configuration. [testng] [2025-01-02 00:36:05,040] [pool-1-thread-12] Initializing /data/julie/biorad/25-65.tif: [testng] 00:36:05,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:36:05,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:05,041 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-02_00-36-05.log] [testng] 00:36:05,042 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53365a7 - End of configuration. [testng] [2025-01-02 00:36:05,419] [pool-1-thread-11] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] 00:36:05,419 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:36:05,420 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:05,420 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-02_00-36-05.log] [testng] 00:36:05,421 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53ad284c - End of configuration. [testng] [2025-01-02 00:36:05,544] [pool-1-thread-10] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] 00:36:05,544 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:36:05,544 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:05,545 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-02_00-36-05.log] [testng] 00:36:05,545 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76336642 - End of configuration. [testng] [2025-01-02 00:36:06,202] [pool-1-thread-9] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] 00:36:06,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:36:06,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:06,203 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-02_00-36-06.log] [testng] 00:36:06,203 |-INFO in ch.qos.logback.core.sift.SiftProcessor@793f891 - End of configuration. [testng] [2025-01-02 00:36:06,221] [pool-1-thread-8] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] 00:36:06,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:36:06,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:06,222 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-02_00-36-06.log] [testng] 00:36:06,223 |-INFO in ch.qos.logback.core.sift.SiftProcessor@640272ee - End of configuration. [testng] [2025-01-02 00:36:06,482] [pool-1-thread-7] Initializing /data/andrey/10310500/10310500.lei: [testng] 00:36:06,483 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:36:06,483 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:06,484 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-02_00-36-06.log] [testng] 00:36:06,485 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b9e3f35 - End of configuration. [testng] [2025-01-02 00:36:06,651] [pool-1-thread-6] Initializing /data/clay/leica_stack.tif: [testng] 00:36:06,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:36:06,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:06,652 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-02_00-36-06.log] [testng] 00:36:06,653 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39994a40 - End of configuration. [testng] [2025-01-02 00:36:06,800] [pool-1-thread-5] Initializing /data/julie/c164_1.tif: [testng] 00:36:06,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:36:06,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:06,801 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-02_00-36-06.log] [testng] 00:36:06,802 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2256ebe3 - End of configuration. [testng] [2025-01-02 00:36:07,590] [pool-1-thread-4] Initializing /data/david/intestine/intestine.lei: [testng] 00:36:07,590 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:36:07,590 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:07,591 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-02_00-36-07.log] [testng] 00:36:07,591 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d520a9f - End of configuration. [testng] [2025-01-02 00:36:07,757] [pool-1-thread-3] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] 00:36:07,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:36:07,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:07,758 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-02_00-36-07.log] [testng] 00:36:07,758 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2cd0b627 - End of configuration. [testng] [2025-01-02 00:36:07,923] [pool-1-thread-2] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] 00:36:07,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:36:07,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:07,924 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-02_00-36-07.log] [testng] 00:36:07,924 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b979eee - End of configuration. [testng] [2025-01-02 00:36:10,870] [pool-1-thread-11] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2025-01-02 00:36:11,307] [pool-1-thread-9] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2025-01-02 00:36:13,606] [pool-1-thread-6] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] [2025-01-02 00:36:15,686] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [2025-01-02 00:36:15,772] [pool-1-thread-12] Initializing /data/samples/Leica_sample.lei: [testng] [2025-01-02 00:36:16,349] [pool-1-thread-6] Initializing /data/david/megan/megan.lei: [testng] [2025-01-02 00:36:19,106] [pool-1-thread-5] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2025-01-02 00:36:20,903] [pool-1-thread-10] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] [2025-01-02 00:36:26,992] [pool-1-thread-12] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2025-01-02 00:36:30,186] [pool-1-thread-12] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2025-01-02 00:36:32,475] [pool-1-thread-12] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2025-01-02 00:36:38,039] [pool-1-thread-10] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2025-01-02 00:38:17,054] [pool-1-thread-11] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2025-01-02 00:38:18,909] [pool-1-thread-11] Initializing /data/brian/tropo/tropo.lei: [testng] [2025-01-02 00:38:39,373] [pool-1-thread-11] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2025-01-02 00:38:40,020] [pool-1-thread-10] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] [2025-01-02 00:38:50,785] [pool-1-thread-10] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2025-01-02 00:38:53,181] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6.lei: [testng] [2025-01-02 00:38:57,241] [pool-1-thread-10] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2025-01-02 00:40:23,991] [pool-1-thread-8] Initializing /data/brian/leica-original/050118.lei: [testng] [2025-01-02 00:41:26,947] [pool-1-thread-4] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2025-01-02 00:42:13,429] [pool-1-thread-6] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2025-01-02 00:42:27,714] [pool-1-thread-9] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] [2025-01-02 00:42:52,851] [pool-1-thread-1] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] [2025-01-02 00:43:05,174] [pool-1-thread-1] Initializing /data/oliver/o459/o459.lei: [testng] [2025-01-02 00:43:14,291] [pool-1-thread-5] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2025-01-02 00:43:39,674] [pool-1-thread-12] Initializing /data/clay/leica_stack.lei: [testng] [2025-01-02 00:43:41,623] [pool-1-thread-4] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2025-01-02 00:43:44,153] [pool-1-thread-4] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2025-01-02 00:43:48,627] [pool-1-thread-11] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] [2025-01-02 00:43:53,171] [pool-1-thread-12] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2025-01-02 00:43:56,991] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2332, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 32 minutes 25 seconds Finished: SUCCESS