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Started by upstream project "BIOFORMATS-test-repo" build number 240 originally caused by: Started by upstream project "Trigger" build number 265 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/jenkins14164952129901296309.sh + '[' leica = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_37675_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 00:21:21,174 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:21:21,175 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 00:21:21,175 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:21:21,176 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:21:21,176 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:21:21,177 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:21:21,177 |-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] 00:21:21,177 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:21:21,177 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:21:21,178 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:21:21,178 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:21:21,178 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:21:21,355 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:21:21,355 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:21:21,379 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:21:21,379 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:21:21,385 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:21:21,385 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:21:21,385 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:21:21,386 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:21:21,386 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 00:21:21,386 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 00:21:21,386 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 209 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-31 00:21:21,395] [main] java.version = 21 [testng] 00:21:21,398 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:21:21,398 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:21,438 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-31_00-21-21.log] [testng] 00:21:21,439 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-10-31 00:21:21,440] [main] testng.directory = /data [testng] [2024-10-31 00:21:21,441] [main] testng.configDirectory = /config [testng] [2024-10-31 00:21:21,449] [main] testng.multiplier = 1.0 [testng] [2024-10-31 00:21:21,458] [main] testng.in-memory = false [testng] [2024-10-31 00:21:21,458] [main] testng.allow-missing = false [testng] [2024-10-31 00:21:21,458] [main] user.language = en [testng] [2024-10-31 00:21:21,458] [main] user.country = ${user.country} [testng] [2024-10-31 00:21:21,458] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-31 00:21:33,387] [main] ---------------------------------------- [testng] [2024-10-31 00:21:33,387] [main] Total files: 5651 [testng] [2024-10-31 00:21:33,387] [main] Scan time: 11.929 s (2 ms/file) [testng] [2024-10-31 00:21:33,388] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-31 00:21:51,602] [pool-1-thread-1] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] 00:21:51,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:21:51,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:51,604 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-31_00-21-51.log] [testng] 00:21:51,605 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21ba70c6 - End of configuration. [testng] [2024-10-31 00:21:51,754] [pool-1-thread-12] Initializing /data/clay/leica_stack.tif: [testng] 00:21:51,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:21:51,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:51,755 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-31_00-21-51.log] [testng] 00:21:51,755 |-INFO in ch.qos.logback.core.sift.SiftProcessor@561c842c - End of configuration. [testng] [2024-10-31 00:21:51,879] [pool-1-thread-11] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] 00:21:51,879 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:21:51,879 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:51,880 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-31_00-21-51.log] [testng] 00:21:51,880 |-INFO in ch.qos.logback.core.sift.SiftProcessor@403fe368 - End of configuration. [testng] [2024-10-31 00:21:52,096] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] 00:21:52,096 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:21:52,096 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:52,097 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-31_00-21-52.log] [testng] 00:21:52,097 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4cbbdc7c - End of configuration. [testng] [2024-10-31 00:21:52,117] [pool-1-thread-9] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] 00:21:52,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:21:52,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:52,118 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-31_00-21-52.log] [testng] 00:21:52,119 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f758f78 - End of configuration. [testng] [2024-10-31 00:21:52,239] [pool-1-thread-8] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] 00:21:52,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:21:52,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:52,239 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-31_00-21-52.log] [testng] 00:21:52,240 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1114faf3 - End of configuration. [testng] [2024-10-31 00:21:52,294] [pool-1-thread-7] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] 00:21:52,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:21:52,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:52,295 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-31_00-21-52.log] [testng] 00:21:52,296 |-INFO in ch.qos.logback.core.sift.SiftProcessor@392bdefa - End of configuration. [testng] [2024-10-31 00:21:52,741] [pool-1-thread-6] Initializing /data/brian/leica-original/050118.lei: [testng] 00:21:52,742 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:21:52,742 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:52,742 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-31_00-21-52.log] [testng] 00:21:52,743 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a43365c - End of configuration. [testng] [2024-10-31 00:21:53,325] [pool-1-thread-5] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] 00:21:53,325 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:21:53,325 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:53,325 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-31_00-21-53.log] [testng] 00:21:53,326 |-INFO in ch.qos.logback.core.sift.SiftProcessor@763dde79 - End of configuration. [testng] [2024-10-31 00:21:53,348] [pool-1-thread-4] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] 00:21:53,348 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:21:53,348 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:53,349 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-31_00-21-53.log] [testng] 00:21:53,350 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bf7b087 - End of configuration. [testng] [2024-10-31 00:21:53,484] [pool-1-thread-3] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] 00:21:53,484 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:21:53,484 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:53,485 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-31_00-21-53.log] [testng] 00:21:53,485 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d040c40 - End of configuration. [testng] [2024-10-31 00:21:53,632] [pool-1-thread-2] Initializing /data/samples/Leica_sample.lei: [testng] 00:21:53,632 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:21:53,632 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:53,633 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-31_00-21-53.log] [testng] 00:21:53,633 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b970c5f - End of configuration. [testng] [2024-10-31 00:21:55,568] [pool-1-thread-8] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2024-10-31 00:21:55,856] [pool-1-thread-5] Initializing /data/david/megan/megan.lei: [testng] [2024-10-31 00:21:56,190] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2024-10-31 00:21:56,677] [pool-1-thread-12] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] [2024-10-31 00:21:57,554] [pool-1-thread-10] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2024-10-31 00:21:58,673] [pool-1-thread-2] Initializing /data/julie/biorad/25-65.tif: [testng] [2024-10-31 00:22:00,512] [pool-1-thread-9] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] [2024-10-31 00:22:03,644] [pool-1-thread-1] Initializing /data/david/intestine/intestine.lei: [testng] [2024-10-31 00:22:04,579] [pool-1-thread-2] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2024-10-31 00:24:07,799] [pool-1-thread-12] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-10-31 00:24:33,920] [pool-1-thread-8] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] [2024-10-31 00:24:37,153] [pool-1-thread-8] Initializing /data/brian/tropo/tropo.lei: [testng] [2024-10-31 00:25:04,216] [pool-1-thread-8] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2024-10-31 00:25:54,363] [pool-1-thread-9] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] [2024-10-31 00:25:55,721] [pool-1-thread-9] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2024-10-31 00:26:01,620] [pool-1-thread-9] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] [2024-10-31 00:26:08,821] [pool-1-thread-9] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2024-10-31 00:26:23,476] [pool-1-thread-4] Initializing /data/clay/leica_stack.lei: [testng] [2024-10-31 00:26:26,040] [pool-1-thread-3] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-10-31 00:26:34,029] [pool-1-thread-4] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2024-10-31 00:26:36,888] [pool-1-thread-10] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2024-10-31 00:26:38,965] [pool-1-thread-1] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2024-10-31 00:26:42,293] [pool-1-thread-10] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2024-10-31 00:26:50,180] [pool-1-thread-8] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2024-10-31 00:26:56,654] [pool-1-thread-5] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-10-31 00:26:59,206] [pool-1-thread-5] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-10-31 00:27:08,864] [pool-1-thread-11] Initializing /data/julie/c164_1.tif: [testng] [2024-10-31 00:27:14,906] [pool-1-thread-11] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-10-31 00:27:16,270] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6.lei: [testng] [2024-10-31 00:27:28,576] [pool-1-thread-8] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-10-31 00:28:06,055] [pool-1-thread-4] Initializing /data/oliver/o459/o459.lei: [testng] [2024-10-31 00:28:47,855] [pool-1-thread-6] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2332, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 38 minutes 50 seconds Finished: SUCCESS