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Started by upstream project "BIOFORMATS-test-repo" build number 282 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/jenkins3414739033456080065.sh + '[' leica = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_44436_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 test-automated: [testng] File leak detector installed [testng] 10:10:55,785 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 10:10:55,787 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 10:10:55,787 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:10:55,788 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:10:55,788 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 10:10:55,788 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 10:10:55,788 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 10:10:55,788 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:10:55,789 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:10:55,789 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 10:10:55,789 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 10:10:55,789 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 10:10:56,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 10:10:56,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 10:10:56,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 10:10:56,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 10:10:56,148 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 10:10:56,148 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 10:10:56,149 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 10:10:56,149 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 10:10:56,149 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 10:10:56,150 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 10:10:56,150 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 361 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-06 10:10:56,160] [main] java.version = 1.8.0_342 [testng] 10:10:56,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 10:10:56,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:10:56,253 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-06_10-10-56.log] [testng] 10:10:56,255 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-06 10:10:56,256] [main] testng.directory = /data [testng] [2024-12-06 10:10:56,257] [main] testng.configDirectory = /config [testng] [2024-12-06 10:10:56,292] [main] testng.multiplier = 1.0 [testng] [2024-12-06 10:10:56,292] [main] testng.in-memory = false [testng] [2024-12-06 10:10:56,292] [main] testng.allow-missing = false [testng] [2024-12-06 10:10:56,292] [main] user.language = en [testng] [2024-12-06 10:10:56,292] [main] user.country = ${user.country} [testng] [2024-12-06 10:10:56,292] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-06 10:11:12,881] [main] ---------------------------------------- [testng] [2024-12-06 10:11:12,882] [main] Total files: 5651 [testng] [2024-12-06 10:11:12,882] [main] Scan time: 16.589 s (2 ms/file) [testng] [2024-12-06 10:11:12,882] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-06 10:12:01,960] [pool-1-thread-1] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] 10:12:01,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 10:12:01,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:12:01,962 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-06_10-12-01.log] [testng] 10:12:01,962 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f48ff9 - End of configuration. [testng] [2024-12-06 10:12:02,452] [pool-1-thread-12] Initializing /data/samples/Leica_sample.lei: [testng] 10:12:02,453 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 10:12:02,453 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:12:02,453 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-06_10-12-02.log] [testng] 10:12:02,454 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79dd0a38 - End of configuration. [testng] [2024-12-06 10:12:02,940] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] 10:12:02,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 10:12:02,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:12:02,941 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-06_10-12-02.log] [testng] 10:12:02,941 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d78f1f6 - End of configuration. [testng] [2024-12-06 10:12:02,981] [pool-1-thread-10] Initializing /data/simon/Leica demo/test/test.lei: [testng] 10:12:02,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 10:12:02,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:12:02,982 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-06_10-12-02.log] [testng] 10:12:02,982 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14d4338c - End of configuration. [testng] [2024-12-06 10:12:03,309] [pool-1-thread-9] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] 10:12:03,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 10:12:03,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:12:03,309 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-06_10-12-03.log] [testng] 10:12:03,310 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e0500e2 - End of configuration. [testng] [2024-12-06 10:12:03,789] [pool-1-thread-8] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] 10:12:03,789 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 10:12:03,790 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:12:03,790 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-06_10-12-03.log] [testng] 10:12:03,791 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ec6ad00 - End of configuration. [testng] [2024-12-06 10:12:04,092] [pool-1-thread-7] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] 10:12:04,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 10:12:04,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:12:04,093 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-06_10-12-04.log] [testng] 10:12:04,093 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a1bc1c9 - End of configuration. [testng] [2024-12-06 10:12:04,139] [pool-1-thread-6] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] 10:12:04,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 10:12:04,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:12:04,140 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-06_10-12-04.log] [testng] 10:12:04,141 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e6b8f85 - End of configuration. [testng] [2024-12-06 10:12:04,190] [pool-1-thread-5] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] 10:12:04,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 10:12:04,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:12:04,191 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-06_10-12-04.log] [testng] 10:12:04,191 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f7faf5c - End of configuration. [testng] [2024-12-06 10:12:04,579] [pool-1-thread-4] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] 10:12:04,579 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 10:12:04,579 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:12:04,579 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-06_10-12-04.log] [testng] 10:12:04,580 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d5a0caa - End of configuration. [testng] [2024-12-06 10:12:04,945] [pool-1-thread-3] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] 10:12:04,945 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 10:12:04,945 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:12:04,945 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-06_10-12-04.log] [testng] 10:12:04,946 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ecdc4a6 - End of configuration. [testng] [2024-12-06 10:12:06,107] [pool-1-thread-2] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] 10:12:06,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 10:12:06,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:12:06,108 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-06_10-12-06.log] [testng] 10:12:06,108 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c94e66 - End of configuration. [testng] [2024-12-06 10:12:09,460] [pool-1-thread-7] Initializing /data/david/megan/megan.lei: [testng] [2024-12-06 10:12:10,546] [pool-1-thread-6] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2024-12-06 10:12:11,481] [pool-1-thread-11] Initializing /data/julie/c164_1.tif: [testng] [2024-12-06 10:12:18,721] [pool-1-thread-2] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2024-12-06 10:12:19,769] [pool-1-thread-12] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2024-12-06 10:12:22,161] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6.lei: [testng] [2024-12-06 10:12:23,059] [pool-1-thread-1] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-12-06 10:12:26,481] [pool-1-thread-1] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-12-06 10:12:30,401] [pool-1-thread-12] Initializing /data/clay/leica_stack.tif: [testng] [2024-12-06 10:12:36,741] [pool-1-thread-12] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2024-12-06 10:13:17,430] [pool-1-thread-6] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2024-12-06 10:13:19,342] [pool-1-thread-6] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-12-06 10:13:21,730] [pool-1-thread-6] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2024-12-06 10:14:48,872] [pool-1-thread-5] Initializing /data/brian/leica-original/050118.lei: [testng] [2024-12-06 10:15:11,863] [pool-1-thread-9] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2024-12-06 10:15:16,046] [pool-1-thread-12] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2024-12-06 10:15:20,169] [pool-1-thread-9] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2024-12-06 10:17:48,353] [pool-1-thread-4] Initializing /data/oliver/o459/o459.lei: [testng] [2024-12-06 10:17:54,271] [pool-1-thread-8] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-12-06 10:18:04,673] [pool-1-thread-11] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] [2024-12-06 10:18:36,597] [pool-1-thread-7] Initializing /data/brian/tropo/tropo.lei: [testng] [2024-12-06 10:18:56,703] [pool-1-thread-7] Initializing /data/clay/leica_stack.lei: [testng] [2024-12-06 10:19:06,633] [pool-1-thread-2] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2024-12-06 10:19:08,441] [pool-1-thread-7] Initializing /data/david/intestine/intestine.lei: [testng] [2024-12-06 10:19:10,112] [pool-1-thread-2] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] [2024-12-06 10:19:30,166] [pool-1-thread-10] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] [2024-12-06 10:19:46,789] [pool-1-thread-10] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2024-12-06 10:20:42,879] [pool-1-thread-8] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-12-06 10:21:36,856] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2024-12-06 10:21:38,649] [pool-1-thread-1] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-12-06 10:22:27,507] [pool-1-thread-3] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] [2024-12-06 10:22:27,698] [pool-1-thread-12] Initializing /data/julie/biorad/25-65.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2332, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 60 minutes 8 seconds Finished: SUCCESS