Started by upstream project "BIOFORMATS-test-repo" build number 249 originally caused by: Started by upstream project "Trigger" build number 273 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/jenkins12413504250853845032.sh + '[' leica = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_39151_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] 00:21:23,220 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:21:23,222 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:21:23,222 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:21:23,223 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:21:23,223 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:21:23,223 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:21:23,224 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:21:23,224 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:21:23,224 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:21:23,224 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:21:23,225 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:21:23,225 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:21:23,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:21:23,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:21:23,475 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:21:23,475 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:21:23,483 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:21:23,483 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:21:23,483 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:21:23,484 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:21:23,484 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:21:23,485 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:21:23,485 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 261 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-08 00:21:23,494] [main] java.version = 1.8.0_342 [testng] 00:21:23,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:21:23,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:23,542 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-08_00-21-23.log] [testng] 00:21:23,544 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-08 00:21:23,546] [main] testng.directory = /data [testng] [2024-11-08 00:21:23,546] [main] testng.configDirectory = /config [testng] [2024-11-08 00:21:23,558] [main] testng.multiplier = 1.0 [testng] [2024-11-08 00:21:23,558] [main] testng.in-memory = false [testng] [2024-11-08 00:21:23,558] [main] testng.allow-missing = false [testng] [2024-11-08 00:21:23,558] [main] user.language = en [testng] [2024-11-08 00:21:23,558] [main] user.country = ${user.country} [testng] [2024-11-08 00:21:23,558] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-08 00:21:38,318] [main] ---------------------------------------- [testng] [2024-11-08 00:21:38,318] [main] Total files: 5651 [testng] [2024-11-08 00:21:38,318] [main] Scan time: 14.76 s (2 ms/file) [testng] [2024-11-08 00:21:38,318] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-08 00:22:09,454] [pool-1-thread-1] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] 00:22:09,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:22:09,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:09,456 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-08_00-22-09.log] [testng] 00:22:09,456 |-INFO in ch.qos.logback.core.sift.SiftProcessor@462ee2ee - End of configuration. [testng] [2024-11-08 00:22:09,807] [pool-1-thread-12] Initializing /data/samples/Leica_sample.lei: [testng] 00:22:09,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:22:09,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:09,808 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-08_00-22-09.log] [testng] 00:22:09,808 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65737daa - End of configuration. [testng] [2024-11-08 00:22:10,120] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] 00:22:10,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:22:10,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:10,121 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-08_00-22-10.log] [testng] 00:22:10,121 |-INFO in ch.qos.logback.core.sift.SiftProcessor@402b884a - End of configuration. [testng] [2024-11-08 00:22:10,173] [pool-1-thread-10] Initializing /data/simon/Leica demo/test/test.lei: [testng] 00:22:10,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:22:10,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:10,174 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-08_00-22-10.log] [testng] 00:22:10,174 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5087137c - End of configuration. [testng] [2024-11-08 00:22:10,619] [pool-1-thread-9] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] 00:22:10,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:22:10,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:10,620 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-08_00-22-10.log] [testng] 00:22:10,621 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b1e0f80 - End of configuration. [testng] [2024-11-08 00:22:11,042] [pool-1-thread-8] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] 00:22:11,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:22:11,043 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:11,043 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-08_00-22-11.log] [testng] 00:22:11,043 |-INFO in ch.qos.logback.core.sift.SiftProcessor@491ed874 - End of configuration. [testng] [2024-11-08 00:22:11,379] [pool-1-thread-7] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] 00:22:11,379 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:22:11,379 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:11,380 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-08_00-22-11.log] [testng] 00:22:11,380 |-INFO in ch.qos.logback.core.sift.SiftProcessor@dd8cde3 - End of configuration. [testng] [2024-11-08 00:22:11,421] [pool-1-thread-6] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] 00:22:11,421 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:22:11,421 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:11,422 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-08_00-22-11.log] [testng] 00:22:11,422 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20e35fa - End of configuration. [testng] [2024-11-08 00:22:11,468] [pool-1-thread-5] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] 00:22:11,468 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:22:11,468 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:11,469 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-08_00-22-11.log] [testng] 00:22:11,469 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a0954a4 - End of configuration. [testng] [2024-11-08 00:22:11,740] [pool-1-thread-4] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] 00:22:11,740 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:22:11,740 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:11,741 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-08_00-22-11.log] [testng] 00:22:11,741 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5239e225 - End of configuration. [testng] [2024-11-08 00:22:12,047] [pool-1-thread-3] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] 00:22:12,047 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:22:12,047 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:12,048 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-08_00-22-12.log] [testng] 00:22:12,048 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14055d4b - End of configuration. [testng] [2024-11-08 00:22:13,217] [pool-1-thread-2] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] 00:22:13,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:22:13,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:13,218 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-08_00-22-13.log] [testng] 00:22:13,218 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b7cbeb - End of configuration. [testng] [2024-11-08 00:22:17,212] [pool-1-thread-7] Initializing /data/david/megan/megan.lei: [testng] [2024-11-08 00:22:17,970] [pool-1-thread-6] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2024-11-08 00:22:18,664] [pool-1-thread-11] Initializing /data/julie/c164_1.tif: [testng] [2024-11-08 00:22:26,689] [pool-1-thread-2] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2024-11-08 00:22:27,958] [pool-1-thread-12] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2024-11-08 00:22:30,422] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6.lei: [testng] [2024-11-08 00:22:31,545] [pool-1-thread-1] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-11-08 00:22:34,516] [pool-1-thread-1] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-11-08 00:22:37,938] [pool-1-thread-12] Initializing /data/clay/leica_stack.tif: [testng] [2024-11-08 00:22:44,163] [pool-1-thread-12] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2024-11-08 00:23:29,462] [pool-1-thread-6] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2024-11-08 00:23:32,212] [pool-1-thread-6] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-11-08 00:23:34,924] [pool-1-thread-6] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2024-11-08 00:24:58,366] [pool-1-thread-5] Initializing /data/brian/leica-original/050118.lei: [testng] [2024-11-08 00:25:22,603] [pool-1-thread-9] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2024-11-08 00:25:27,021] [pool-1-thread-12] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2024-11-08 00:25:32,501] [pool-1-thread-9] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2024-11-08 00:29:10,857] [pool-1-thread-4] Initializing /data/oliver/o459/o459.lei: [testng] [2024-11-08 00:29:18,287] [pool-1-thread-8] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-11-08 00:29:23,312] [pool-1-thread-11] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] [2024-11-08 00:29:53,943] [pool-1-thread-7] Initializing /data/brian/tropo/tropo.lei: [testng] [2024-11-08 00:30:13,827] [pool-1-thread-7] Initializing /data/clay/leica_stack.lei: [testng] [2024-11-08 00:30:25,068] [pool-1-thread-2] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2024-11-08 00:30:26,567] [pool-1-thread-7] Initializing /data/david/intestine/intestine.lei: [testng] [2024-11-08 00:30:27,987] [pool-1-thread-2] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] [2024-11-08 00:30:49,963] [pool-1-thread-10] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] [2024-11-08 00:31:09,745] [pool-1-thread-10] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2024-11-08 00:32:02,923] [pool-1-thread-8] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-11-08 00:33:07,360] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2024-11-08 00:33:10,363] [pool-1-thread-1] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-11-08 00:34:09,867] [pool-1-thread-3] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] [2024-11-08 00:34:12,433] [pool-1-thread-3] 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: 51 minutes 46 seconds Finished: SUCCESS