Started by upstream project "BIOFORMATS-test-repo" build number 285 originally caused by: Started by upstream project "Trigger" build number 304 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/jenkins18440972446350857290.sh + '[' leica = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_44928_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 -Duser.language=fr -Duser.country=FR 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] 00:22:08,440 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:22:08,442 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:22:08,442 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:22:08,443 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:22:08,443 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:22:08,443 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:22:08,443 |-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] 00:22:08,443 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:22:08,444 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:22:08,444 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:22:08,444 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:22:08,444 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:22:08,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:22:08,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:22:08,679 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:22:08,679 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:22:08,705 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:22:08,705 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:22:08,705 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:22:08,705 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:22:08,705 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:22:08,706 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:22:08,706 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 262 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-09 00:22:08,716] [main] java.version = 1.8.0_342 [testng] 00:22:08,719 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:22:08,719 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:08,765 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-09_00-22-08.log] [testng] 00:22:08,766 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-09 00:22:08,768] [main] testng.directory = /data [testng] [2024-12-09 00:22:08,769] [main] testng.configDirectory = /config [testng] [2024-12-09 00:22:08,781] [main] testng.multiplier = 1.0 [testng] [2024-12-09 00:22:08,781] [main] testng.in-memory = false [testng] [2024-12-09 00:22:08,781] [main] testng.allow-missing = false [testng] [2024-12-09 00:22:08,781] [main] user.language = fr [testng] [2024-12-09 00:22:08,781] [main] user.country = FR [testng] [2024-12-09 00:22:08,781] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-09 00:22:23,637] [main] ---------------------------------------- [testng] [2024-12-09 00:22:23,637] [main] Total files: 5651 [testng] [2024-12-09 00:22:23,638] [main] Scan time: 14.856 s (2 ms/file) [testng] [2024-12-09 00:22:23,638] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-09 00:22:48,939] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] 00:22:48,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:22:48,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:48,941 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-09_00-22-48.log] [testng] 00:22:48,941 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a727568 - End of configuration. [testng] [2024-12-09 00:22:48,970] [pool-1-thread-12] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] 00:22:48,970 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:22:48,970 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:48,971 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-09_00-22-48.log] [testng] 00:22:48,971 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f94596 - End of configuration. [testng] [2024-12-09 00:22:49,660] [pool-1-thread-11] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] 00:22:49,660 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:22:49,660 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:49,662 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-09_00-22-49.log] [testng] 00:22:49,663 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2239ae61 - End of configuration. [testng] [2024-12-09 00:22:49,843] [pool-1-thread-10] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] 00:22:49,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:22:49,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:49,845 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-09_00-22-49.log] [testng] 00:22:49,845 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3600653e - End of configuration. [testng] [2024-12-09 00:22:50,033] [pool-1-thread-9] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] 00:22:50,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:22:50,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:50,034 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-09_00-22-50.log] [testng] 00:22:50,034 |-INFO in ch.qos.logback.core.sift.SiftProcessor@745de567 - End of configuration. [testng] [2024-12-09 00:22:51,050] [pool-1-thread-8] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] 00:22:51,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:22:51,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:51,051 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-09_00-22-51.log] [testng] 00:22:51,051 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79a2be07 - End of configuration. [testng] [2024-12-09 00:22:51,238] [pool-1-thread-7] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] 00:22:51,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:22:51,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:51,240 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-09_00-22-51.log] [testng] 00:22:51,240 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66f813 - End of configuration. [testng] [2024-12-09 00:22:51,270] [pool-1-thread-6] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] 00:22:51,271 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:22:51,271 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:51,271 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-09_00-22-51.log] [testng] 00:22:51,272 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ae2ff9f - End of configuration. [testng] [2024-12-09 00:22:51,571] [pool-1-thread-5] Initializing /data/brian/tropo/tropo.lei: [testng] 00:22:51,571 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:22:51,571 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:51,572 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-09_00-22-51.log] [testng] 00:22:51,572 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f8e8a0c - End of configuration. [testng] [2024-12-09 00:22:52,288] [pool-1-thread-4] Initializing /data/oliver/o459/o459.lei: [testng] 00:22:52,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:22:52,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:52,289 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-09_00-22-52.log] [testng] 00:22:52,289 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5012f03f - End of configuration. [testng] [2024-12-09 00:22:52,808] [pool-1-thread-3] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] 00:22:52,808 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:22:52,808 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:52,809 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-09_00-22-52.log] [testng] 00:22:52,809 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fa35fc1 - End of configuration. [testng] [2024-12-09 00:22:53,032] [pool-1-thread-2] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] 00:22:53,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:22:53,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:53,033 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-09_00-22-53.log] [testng] 00:22:53,033 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28f63e13 - End of configuration. [testng] [2024-12-09 00:22:57,273] [pool-1-thread-2] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-12-09 00:22:57,372] [pool-1-thread-1] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2024-12-09 00:22:59,032] [pool-1-thread-7] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2024-12-09 00:23:01,169] [pool-1-thread-7] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2024-12-09 00:23:01,816] [pool-1-thread-2] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2024-12-09 00:23:03,521] [pool-1-thread-8] Initializing /data/clay/leica_stack.lei: [testng] [2024-12-09 00:23:04,724] [pool-1-thread-2] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2024-12-09 00:23:09,991] [pool-1-thread-10] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-12-09 00:23:13,741] [pool-1-thread-6] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2024-12-09 00:23:16,109] [pool-1-thread-5] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2024-12-09 00:23:19,398] [pool-1-thread-8] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2024-12-09 00:25:20,027] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [2024-12-09 00:25:24,122] [pool-1-thread-3] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] [2024-12-09 00:25:45,294] [pool-1-thread-6] Initializing /data/julie/c164_1.tif: [testng] [2024-12-09 00:25:54,470] [pool-1-thread-6] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-12-09 00:26:20,955] [pool-1-thread-7] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] [2024-12-09 00:29:01,339] [pool-1-thread-11] Initializing /data/julie/biorad/25-65.tif: [testng] [2024-12-09 00:29:08,201] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6.lei: [testng] [2024-12-09 00:29:26,730] [pool-1-thread-7] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2024-12-09 00:29:32,301] [pool-1-thread-7] Initializing /data/clay/leica_stack.tif: [testng] [2024-12-09 00:29:36,475] [pool-1-thread-7] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-12-09 00:29:48,645] [pool-1-thread-9] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2024-12-09 00:30:04,882] [pool-1-thread-3] Initializing /data/samples/Leica_sample.lei: [testng] [2024-12-09 00:30:11,787] [pool-1-thread-3] Initializing /data/david/megan/megan.lei: [testng] [2024-12-09 00:30:39,262] [pool-1-thread-5] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-12-09 00:31:09,020] [pool-1-thread-8] Initializing /data/david/intestine/intestine.lei: [testng] [2024-12-09 00:31:54,275] [pool-1-thread-7] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2024-12-09 00:32:09,734] [pool-1-thread-10] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-12-09 00:32:12,115] [pool-1-thread-10] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2024-12-09 00:32:17,572] [pool-1-thread-10] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] [2024-12-09 00:32:31,334] [pool-1-thread-12] Initializing /data/brian/leica-original/050118.lei: [testng] [2024-12-09 00:32:38,105] [pool-1-thread-7] Initializing /data/constantin/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: 35 minutes 8 seconds Finished: SUCCESS