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Started by upstream project "BIOFORMATS-test-repo" build number 7 originally caused by: Started by upstream project "Trigger" build number 10 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/jenkins16737173536000696668.sh + '[' leica = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_953_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 00:17:36,870 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:17:36,872 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 00:17:36,872 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:17:36,872 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:17:36,873 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:17:36,873 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:17:36,873 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:17:36,873 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:17:36,874 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:17:36,874 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:17:36,875 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:17:36,875 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:17:37,040 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:17:37,040 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:17:37,064 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:17:37,064 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:17:37,070 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:17:37,070 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:17:37,070 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:17:37,071 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:17:37,071 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 00:17:37,071 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 00:17:37,072 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 198 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-21 00:17:37,080] [main] java.version = 21 [testng] 00:17:37,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:17:37,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:17:37,123 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-21_00-17-37.log] [testng] 00:17:37,124 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-03-21 00:17:37,126] [main] testng.directory = /data [testng] [2024-03-21 00:17:37,126] [main] testng.configDirectory = /config [testng] [2024-03-21 00:17:37,134] [main] testng.multiplier = 1.0 [testng] [2024-03-21 00:17:37,135] [main] testng.in-memory = false [testng] [2024-03-21 00:17:37,135] [main] testng.allow-missing = false [testng] [2024-03-21 00:17:37,135] [main] user.language = en [testng] [2024-03-21 00:17:37,135] [main] user.country = ${user.country} [testng] [2024-03-21 00:17:37,135] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-21 00:17:49,233] [main] ---------------------------------------- [testng] [2024-03-21 00:17:49,233] [main] Total files: 5651 [testng] [2024-03-21 00:17:49,234] [main] Scan time: 12.098 s (2 ms/file) [testng] [2024-03-21 00:17:49,234] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-21 00:18:12,764] [pool-1-thread-1] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] 00:18:12,764 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:18:12,764 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:18:12,766 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-21_00-18-12.log] [testng] 00:18:12,766 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2881f6cd - End of configuration. [testng] [2024-03-21 00:18:12,838] [pool-1-thread-12] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] 00:18:12,838 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:18:12,838 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:18:12,839 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-21_00-18-12.log] [testng] 00:18:12,840 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4580ce56 - End of configuration. [testng] [2024-03-21 00:18:12,887] [pool-1-thread-11] Initializing /data/stjude/NIHSSE02-3.lei: [testng] 00:18:12,887 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:18:12,887 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:18:12,888 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-21_00-18-12.log] [testng] 00:18:12,888 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50ca68ba - End of configuration. [testng] [2024-03-21 00:18:12,950] [pool-1-thread-10] Initializing /data/david/intestine/intestine.lei: [testng] 00:18:12,950 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:18:12,950 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:18:12,951 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-21_00-18-12.log] [testng] 00:18:12,952 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b6efb11 - End of configuration. [testng] [2024-03-21 00:18:13,025] [pool-1-thread-9] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] 00:18:13,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:18:13,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:18:13,027 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-21_00-18-13.log] [testng] 00:18:13,027 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5994a432 - End of configuration. [testng] [2024-03-21 00:18:13,039] [pool-1-thread-8] Initializing /data/oliver/o459/o459.lei: [testng] 00:18:13,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:18:13,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:18:13,040 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-21_00-18-13.log] [testng] 00:18:13,040 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2878f3fa - End of configuration. [testng] [2024-03-21 00:18:13,272] [pool-1-thread-7] Initializing /data/simon/Leica demo/test/test.lei: [testng] 00:18:13,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:18:13,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:18:13,273 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-21_00-18-13.log] [testng] 00:18:13,273 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56df5d44 - End of configuration. [testng] [2024-03-21 00:18:13,423] [pool-1-thread-6] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] 00:18:13,423 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:18:13,423 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:18:13,424 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-21_00-18-13.log] [testng] 00:18:13,424 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e8325aa - End of configuration. [testng] [2024-03-21 00:18:13,460] [pool-1-thread-5] Initializing /data/vytas/4voxels/4voxels.lei: [testng] 00:18:13,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:18:13,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:18:13,462 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-21_00-18-13.log] [testng] 00:18:13,462 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d897584 - End of configuration. [testng] [2024-03-21 00:18:13,561] [pool-1-thread-4] Initializing /data/julie/biorad/25-65.tif: [testng] 00:18:13,561 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:18:13,561 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:18:13,562 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-21_00-18-13.log] [testng] 00:18:13,563 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f9f9fec - End of configuration. [testng] [2024-03-21 00:18:13,661] [pool-1-thread-3] Initializing /data/david/megan/megan.lei: [testng] 00:18:13,661 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:18:13,661 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:18:13,662 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-21_00-18-13.log] [testng] 00:18:13,662 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1cf726f2 - End of configuration. [testng] [2024-03-21 00:18:13,761] [pool-1-thread-2] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] 00:18:13,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:18:13,762 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:18:13,762 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-21_00-18-13.log] [testng] 00:18:13,763 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24b4302 - End of configuration. [testng] [2024-03-21 00:18:15,491] [pool-1-thread-9] Initializing /data/brian/tropo/tropo.lei: [testng] [2024-03-21 00:18:16,433] [pool-1-thread-4] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2024-03-21 00:18:16,771] [pool-1-thread-1] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2024-03-21 00:18:18,052] [pool-1-thread-12] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2024-03-21 00:18:18,821] [pool-1-thread-12] Initializing /data/brian/leica-original/050118.lei: [testng] [2024-03-21 00:18:19,964] [pool-1-thread-1] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-03-21 00:18:20,850] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [2024-03-21 00:18:21,491] [pool-1-thread-9] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2024-03-21 00:18:21,755] [pool-1-thread-1] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-03-21 00:18:31,196] [pool-1-thread-11] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-03-21 00:18:32,264] [pool-1-thread-11] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2024-03-21 00:18:59,445] [pool-1-thread-4] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-03-21 00:19:08,899] [pool-1-thread-2] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] [2024-03-21 00:19:12,912] [pool-1-thread-6] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] [2024-03-21 00:19:15,947] [pool-1-thread-6] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] [2024-03-21 00:20:13,941] [pool-1-thread-2] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2024-03-21 00:20:16,698] [pool-1-thread-9] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2024-03-21 00:20:18,520] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2024-03-21 00:20:19,295] [pool-1-thread-10] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2024-03-21 00:20:20,819] [pool-1-thread-3] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] [2024-03-21 00:20:26,953] [pool-1-thread-3] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2024-03-21 00:20:40,194] [pool-1-thread-7] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] [2024-03-21 00:20:40,915] [pool-1-thread-7] Initializing /data/constantin/cell6/cell6.lei: [testng] [2024-03-21 00:21:00,119] [pool-1-thread-9] Initializing /data/julie/c164_1.tif: [testng] [2024-03-21 00:21:02,877] [pool-1-thread-6] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2024-03-21 00:21:05,686] [pool-1-thread-9] Initializing /data/clay/leica_stack.lei: [testng] [2024-03-21 00:21:09,497] [pool-1-thread-9] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2024-03-21 00:21:28,529] [pool-1-thread-4] Initializing /data/samples/Leica_sample.lei: [testng] [2024-03-21 00:21:30,367] [pool-1-thread-4] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] [2024-03-21 00:21:42,694] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2024-03-21 00:21:43,737] [pool-1-thread-1] Initializing /data/clay/leica_stack.tif: [testng] [2024-03-21 00:21:45,075] [pool-1-thread-1] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2332, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 10 minutes 58 seconds Finished: SUCCESS