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Started by upstream project "BIOFORMATS-test-repo" build number 212 originally caused by: Started by upstream project "Trigger" build number 238 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/jenkins12268531597853096717.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_33599_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] 01:22:22,984 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:22:22,986 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 01:22:22,986 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:22:22,987 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:22:22,988 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:22:22,988 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:22:22,988 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:22:22,988 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:22:22,989 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:22:22,989 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:22:22,989 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:22:22,989 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:22:23,220 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:22:23,220 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:22:23,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:22:23,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:22:23,271 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:22:23,271 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:22:23,271 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:22:23,272 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:22:23,272 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 01:22:23,273 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 01:22:23,273 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 284 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-07 01:22:23,282] [main] java.version = 1.8.0_342 [testng] 01:22:23,286 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:22:23,286 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:23,331 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-07_01-22-23.log] [testng] 01:22:23,333 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-10-07 01:22:23,335] [main] testng.directory = /data [testng] [2024-10-07 01:22:23,335] [main] testng.configDirectory = /config [testng] [2024-10-07 01:22:23,346] [main] testng.multiplier = 1.0 [testng] [2024-10-07 01:22:23,347] [main] testng.in-memory = false [testng] [2024-10-07 01:22:23,347] [main] testng.allow-missing = false [testng] [2024-10-07 01:22:23,347] [main] user.language = fr [testng] [2024-10-07 01:22:23,347] [main] user.country = FR [testng] [2024-10-07 01:22:23,347] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-07 01:22:33,741] [main] ---------------------------------------- [testng] [2024-10-07 01:22:33,741] [main] Total files: 5651 [testng] [2024-10-07 01:22:33,741] [main] Scan time: 10.394 s (1 ms/file) [testng] [2024-10-07 01:22:33,741] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-07 01:22:50,581] [pool-1-thread-1] Initializing /data/andrey/10310500/10310500.lei: [testng] 01:22:50,582 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:22:50,582 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:50,583 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-07_01-22-50.log] [testng] 01:22:50,584 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c668cdd - End of configuration. [testng] [2024-10-07 01:22:50,687] [pool-1-thread-12] Initializing /data/julie/biorad/25-65.tif: [testng] 01:22:50,688 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:22:50,688 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:50,689 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-07_01-22-50.log] [testng] 01:22:50,689 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f6e190b - End of configuration. [testng] [2024-10-07 01:22:50,792] [pool-1-thread-11] Initializing /data/clay/leica_stack.tif: [testng] 01:22:50,792 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:22:50,792 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:50,793 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-07_01-22-50.log] [testng] 01:22:50,793 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d535628 - End of configuration. [testng] [2024-10-07 01:22:50,850] [pool-1-thread-10] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] 01:22:50,850 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:22:50,851 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:50,851 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-07_01-22-50.log] [testng] 01:22:50,852 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bc63bf8 - End of configuration. [testng] [2024-10-07 01:22:50,921] [pool-1-thread-9] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] 01:22:50,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:22:50,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:50,922 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-07_01-22-50.log] [testng] 01:22:50,922 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4172db03 - End of configuration. [testng] [2024-10-07 01:22:51,066] [pool-1-thread-8] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] 01:22:51,066 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:22:51,066 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:51,067 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-07_01-22-51.log] [testng] 01:22:51,067 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6dd30782 - End of configuration. [testng] [2024-10-07 01:22:51,082] [pool-1-thread-7] Initializing /data/samples/Leica_sample.lei: [testng] 01:22:51,082 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:22:51,082 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:51,083 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-07_01-22-51.log] [testng] 01:22:51,083 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17b34e86 - End of configuration. [testng] [2024-10-07 01:22:51,142] [pool-1-thread-6] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] 01:22:51,142 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:22:51,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:51,143 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-07_01-22-51.log] [testng] 01:22:51,143 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7cddc8cb - End of configuration. [testng] [2024-10-07 01:22:51,264] [pool-1-thread-5] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] 01:22:51,264 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:22:51,264 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:51,265 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-07_01-22-51.log] [testng] 01:22:51,265 |-INFO in ch.qos.logback.core.sift.SiftProcessor@460a54a9 - End of configuration. [testng] [2024-10-07 01:22:51,343] [pool-1-thread-4] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] 01:22:51,344 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:22:51,344 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:51,344 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-07_01-22-51.log] [testng] 01:22:51,344 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6efa45c9 - End of configuration. [testng] [2024-10-07 01:22:51,465] [pool-1-thread-3] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] 01:22:51,465 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:22:51,465 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:51,466 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-07_01-22-51.log] [testng] 01:22:51,466 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d26046c - End of configuration. [testng] [2024-10-07 01:22:51,482] [pool-1-thread-2] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] 01:22:51,483 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:22:51,483 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:51,483 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-07_01-22-51.log] [testng] 01:22:51,484 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d8e270 - End of configuration. [testng] [2024-10-07 01:22:52,991] [pool-1-thread-8] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2024-10-07 01:22:53,176] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [2024-10-07 01:22:53,210] [pool-1-thread-2] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] [2024-10-07 01:22:53,260] [pool-1-thread-11] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2024-10-07 01:22:54,291] [pool-1-thread-12] Initializing /data/oliver/o459/o459.lei: [testng] [2024-10-07 01:22:54,573] [pool-1-thread-3] Initializing /data/brian/tropo/tropo.lei: [testng] [2024-10-07 01:22:54,869] [pool-1-thread-2] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-10-07 01:22:54,915] [pool-1-thread-4] Initializing /data/constantin/cell6/cell6.lei: [testng] [2024-10-07 01:22:55,194] [pool-1-thread-6] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2024-10-07 01:22:56,246] [pool-1-thread-7] Initializing /data/clay/leica_stack.lei: [testng] [2024-10-07 01:22:56,870] [pool-1-thread-2] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-10-07 01:23:01,575] [pool-1-thread-7] Initializing /data/brian/leica-original/050118.lei: [testng] [2024-10-07 01:23:04,418] [pool-1-thread-3] Initializing /data/david/intestine/intestine.lei: [testng] [2024-10-07 01:23:19,500] [pool-1-thread-8] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] [2024-10-07 01:24:34,724] [pool-1-thread-11] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2024-10-07 01:24:58,404] [pool-1-thread-8] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2024-10-07 01:25:20,055] [pool-1-thread-5] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2024-10-07 01:26:02,057] [pool-1-thread-10] Initializing /data/julie/c164_1.tif: [testng] [2024-10-07 01:26:08,669] [pool-1-thread-10] Initializing /data/david/megan/megan.lei: [testng] [2024-10-07 01:26:11,657] [pool-1-thread-4] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2024-10-07 01:26:29,705] [pool-1-thread-3] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2024-10-07 01:26:42,166] [pool-1-thread-9] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-10-07 01:26:43,831] [pool-1-thread-9] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2024-10-07 01:27:40,420] [pool-1-thread-3] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] [2024-10-07 01:27:44,984] [pool-1-thread-3] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-10-07 01:28:01,117] [pool-1-thread-8] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2024-10-07 01:28:03,196] [pool-1-thread-1] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-10-07 01:28:22,249] [pool-1-thread-7] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] [2024-10-07 01:28:24,536] [pool-1-thread-7] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] [2024-10-07 01:28:31,090] [pool-1-thread-7] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] [2024-10-07 01:28:39,508] [pool-1-thread-7] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2024-10-07 01:29:03,591] [pool-1-thread-10] Initializing /data/constantin/cell6/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: 18 minutes 32 seconds Finished: SUCCESS